Starting phenix.real_space_refine on Wed Feb 14 04:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejc_28177/02_2024/8ejc_28177_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 50 5.16 5 C 5506 2.51 5 N 1489 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "R TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8659 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1877 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2572 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 406 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2020 Unusual residues: {'2YB': 1} Classifications: {'peptide': 271, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 250, None: 1} Not linked: pdbres="LEU R 279 " pdbres="2YB R 401 " Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 5.04, per 1000 atoms: 0.58 Number of scatterers: 8659 At special positions: 0 Unit cell: (96.3, 115.56, 129.47, 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 50 16.00 O 1614 8.00 N 1489 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 34.8% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.620A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.915A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.593A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 4.306A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'R' and resid 5 through 36 Proline residue: R 21 - end of helix removed outlier: 4.197A pdb=" N LEU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 67 Proline residue: R 60 - end of helix Processing helix chain 'R' and resid 76 through 109 removed outlier: 3.516A pdb=" N CYS R 79 " --> pdb=" O ALA R 76 " (cutoff:3.500A) Proline residue: R 80 - end of helix removed outlier: 5.291A pdb=" N PHE R 88 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Proline residue: R 89 - end of helix removed outlier: 3.616A pdb=" N ALA R 109 " --> pdb=" O LEU R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 117 Processing helix chain 'R' and resid 120 through 143 Processing helix chain 'R' and resid 176 through 211 Proline residue: R 181 - end of helix removed outlier: 4.919A pdb=" N LEU R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Proline residue: R 194 - end of helix Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 237 through 249 Processing helix chain 'R' and resid 256 through 276 removed outlier: 4.118A pdb=" N VAL R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 203 through 207 removed outlier: 7.359A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS A 206 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 133 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 97 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.845A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.828A 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: 6.985A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.938A 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: 6.769A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.982A 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: 6.727A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.162A 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: 6.763A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.822A 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: 6.570A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.695A 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: 6.779A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 95 through 99 removed outlier: 5.253A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 150 removed outlier: 6.566A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2831 1.34 - 1.46: 2186 1.46 - 1.58: 3770 1.58 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 8855 Sorted by residual: bond pdb=" C27 2YB R 401 " pdb=" C28 2YB R 401 " ideal model delta sigma weight residual 1.505 1.384 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1 2YB R 401 " pdb=" C2 2YB R 401 " ideal model delta sigma weight residual 1.503 1.391 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C14 2YB R 401 " pdb=" C15 2YB R 401 " ideal model delta sigma weight residual 1.502 1.390 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C21 2YB R 401 " pdb=" C22 2YB R 401 " ideal model delta sigma weight residual 1.498 1.391 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C16 2YB R 401 " pdb=" C17 2YB R 401 " ideal model delta sigma weight residual 1.485 1.394 0.091 2.00e-02 2.50e+03 2.05e+01 ... (remaining 8850 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.12: 252 107.12 - 113.88: 4961 113.88 - 120.64: 3639 120.64 - 127.40: 3081 127.40 - 134.17: 109 Bond angle restraints: 12042 Sorted by residual: angle pdb=" CA TRP R 131 " pdb=" CB TRP R 131 " pdb=" CG TRP R 131 " ideal model delta sigma weight residual 113.60 119.94 -6.34 1.90e+00 2.77e-01 1.11e+01 angle pdb=" O11 2YB R 401 " pdb=" S9 2YB R 401 " pdb=" O12 2YB R 401 " ideal model delta sigma weight residual 117.70 109.58 8.12 3.00e+00 1.11e-01 7.33e+00 angle pdb=" N GLU A 171 " pdb=" CA GLU A 171 " pdb=" C GLU A 171 " ideal model delta sigma weight residual 109.81 115.39 -5.58 2.21e+00 2.05e-01 6.37e+00 angle pdb=" C22 2YB R 401 " pdb=" O23 2YB R 401 " pdb=" C24 2YB R 401 " ideal model delta sigma weight residual 118.60 111.15 7.45 3.00e+00 1.11e-01 6.17e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 121.85 117.88 3.97 1.77e+00 3.19e-01 5.03e+00 ... (remaining 12037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.52: 4962 24.52 - 49.04: 224 49.04 - 73.56: 18 73.56 - 98.08: 3 98.08 - 122.60: 1 Dihedral angle restraints: 5208 sinusoidal: 1958 harmonic: 3250 Sorted by residual: dihedral pdb=" CA GLY B 141 " pdb=" C GLY B 141 " pdb=" N HIS B 142 " pdb=" CA HIS B 142 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLY B 182 " pdb=" C GLY B 182 " pdb=" N HIS B 183 " pdb=" CA HIS B 183 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C8 2YB R 401 " pdb=" C6 2YB R 401 " pdb=" C7 2YB R 401 " pdb=" O5 2YB R 401 " ideal model delta sinusoidal sigma weight residual 180.08 57.48 122.60 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 824 0.034 - 0.068: 367 0.068 - 0.102: 113 0.102 - 0.136: 48 0.136 - 0.170: 4 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CB THR E 172 " pdb=" CA THR E 172 " pdb=" OG1 THR E 172 " pdb=" CG2 THR E 172 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" CG LEU R 11 " pdb=" CB LEU R 11 " pdb=" CD1 LEU R 11 " pdb=" CD2 LEU R 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1353 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 238 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO R 239 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 131 " 0.014 2.00e-02 2.50e+03 1.07e-02 2.86e+00 pdb=" CG TRP R 131 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP R 131 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 131 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 131 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 131 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 131 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 131 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 131 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 236 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 858 2.74 - 3.28: 8760 3.28 - 3.82: 14624 3.82 - 4.36: 17312 4.36 - 4.90: 29811 Nonbonded interactions: 71365 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.199 2.520 nonbonded pdb=" OE2 GLU A 234 " pdb=" NH1 ARG R 118 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.232 2.440 nonbonded pdb=" OG SER C 57 " pdb=" OE1 GLU C 58 " model vdw 2.255 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.317 2.440 ... (remaining 71360 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: 0.380 Set stop_for_unknowns flag: 0.010 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: 2.260 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.280 Find NCS groups from input model: 0.590 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: 0.020 Load rotamer database and sin/cos tables:17.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 0.121 8855 Z= 0.353 Angle : 0.645 8.121 12042 Z= 0.323 Chirality : 0.044 0.170 1356 Planarity : 0.004 0.052 1543 Dihedral : 13.368 122.600 3119 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.26), residues: 1118 helix: 2.17 (0.26), residues: 375 sheet: 0.40 (0.32), residues: 294 loop : -0.02 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 131 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE B 253 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: B 17 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 32 LYS cc_start: 0.8887 (tttm) cc_final: 0.8540 (tttm) REVERT: E 93 MET cc_start: 0.7848 (tpt) cc_final: 0.7597 (tpt) REVERT: E 201 ASP cc_start: 0.7962 (p0) cc_final: 0.7738 (t70) REVERT: R 137 HIS cc_start: 0.8206 (t-90) cc_final: 0.7843 (t-90) REVERT: R 170 CYS cc_start: 0.7786 (m) cc_final: 0.7584 (m) REVERT: R 240 TYR cc_start: 0.8514 (t80) cc_final: 0.8231 (t80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.2444 time to fit residues: 213.1216 Evaluate side-chains 117 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 16 ASN B 36 ASN E 77 ASN R 115 GLN R 241 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8855 Z= 0.212 Angle : 0.561 7.926 12042 Z= 0.287 Chirality : 0.042 0.134 1356 Planarity : 0.004 0.051 1543 Dihedral : 5.290 88.918 1249 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.33 % Allowed : 10.96 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1118 helix: 2.26 (0.27), residues: 375 sheet: 0.56 (0.32), residues: 293 loop : -0.11 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 131 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE B 253 TYR 0.009 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.070 Fit side-chains REVERT: A 25 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: B 57 LYS cc_start: 0.8144 (pttm) cc_final: 0.7942 (ptpp) REVERT: B 175 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: E 163 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: E 201 ASP cc_start: 0.8025 (p0) cc_final: 0.7740 (t70) REVERT: R 53 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8479 (tp) REVERT: R 137 HIS cc_start: 0.8235 (t-90) cc_final: 0.7849 (t-90) REVERT: R 170 CYS cc_start: 0.7920 (m) cc_final: 0.7661 (m) REVERT: R 221 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6218 (ttm170) REVERT: R 240 TYR cc_start: 0.8510 (t80) cc_final: 0.8218 (t80) outliers start: 21 outliers final: 8 residues processed: 137 average time/residue: 1.2258 time to fit residues: 179.3974 Evaluate side-chains 131 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 232 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 100 optimal weight: 0.0040 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN B 16 ASN B 36 ASN B 75 GLN C 11 GLN E 183 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 115 GLN R 241 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8855 Z= 0.229 Angle : 0.558 8.194 12042 Z= 0.285 Chirality : 0.042 0.136 1356 Planarity : 0.004 0.052 1543 Dihedral : 5.197 76.620 1249 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.54 % Allowed : 12.62 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.26), residues: 1118 helix: 2.16 (0.27), residues: 374 sheet: 0.61 (0.33), residues: 280 loop : -0.16 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 131 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE B 253 TYR 0.014 0.001 TYR A 204 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.433 Fit side-chains REVERT: A 25 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: B 175 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: E 19 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8758 (tttm) REVERT: E 51 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8497 (tp) REVERT: E 201 ASP cc_start: 0.8045 (p0) cc_final: 0.7733 (t70) REVERT: R 53 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8597 (tp) REVERT: R 137 HIS cc_start: 0.8180 (t-90) cc_final: 0.7842 (t-90) REVERT: R 221 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6210 (ttm170) REVERT: R 240 TYR cc_start: 0.8531 (t80) cc_final: 0.8207 (t80) outliers start: 32 outliers final: 12 residues processed: 136 average time/residue: 1.1178 time to fit residues: 162.7413 Evaluate side-chains 129 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 221 ARG Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 229 GLN B 16 ASN B 36 ASN B 220 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8855 Z= 0.147 Angle : 0.520 8.406 12042 Z= 0.264 Chirality : 0.040 0.139 1356 Planarity : 0.004 0.054 1543 Dihedral : 4.864 66.004 1249 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.88 % Allowed : 16.28 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.31 (0.26), residues: 1118 helix: 2.28 (0.27), residues: 371 sheet: 0.71 (0.34), residues: 266 loop : -0.12 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 131 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR A 204 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.205 Fit side-chains REVERT: B 175 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: E 201 ASP cc_start: 0.8051 (p0) cc_final: 0.7727 (t70) REVERT: R 53 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8592 (tp) REVERT: R 137 HIS cc_start: 0.8103 (t-90) cc_final: 0.7793 (t-90) REVERT: R 170 CYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6883 (m) outliers start: 26 outliers final: 10 residues processed: 135 average time/residue: 1.1091 time to fit residues: 160.5033 Evaluate side-chains 129 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.0010 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 75 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8855 Z= 0.164 Angle : 0.526 8.575 12042 Z= 0.268 Chirality : 0.040 0.138 1356 Planarity : 0.004 0.053 1543 Dihedral : 4.768 58.531 1249 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.21 % Allowed : 17.28 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.34 (0.26), residues: 1118 helix: 2.31 (0.27), residues: 371 sheet: 0.72 (0.34), residues: 266 loop : -0.09 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 131 HIS 0.003 0.001 HIS B 142 PHE 0.011 0.001 PHE B 253 TYR 0.011 0.001 TYR A 204 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8541 (tptp) cc_final: 0.8091 (tmtt) REVERT: B 175 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: E 19 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8783 (tttm) REVERT: E 51 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8391 (tp) REVERT: E 201 ASP cc_start: 0.8041 (p0) cc_final: 0.7687 (t70) REVERT: R 137 HIS cc_start: 0.8063 (t-90) cc_final: 0.7819 (t-90) REVERT: R 170 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6924 (m) outliers start: 29 outliers final: 12 residues processed: 141 average time/residue: 1.1652 time to fit residues: 175.4387 Evaluate side-chains 131 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 36 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN R 115 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8855 Z= 0.172 Angle : 0.536 8.744 12042 Z= 0.272 Chirality : 0.040 0.138 1356 Planarity : 0.004 0.053 1543 Dihedral : 4.796 64.236 1249 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.77 % Allowed : 18.27 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.35 (0.26), residues: 1118 helix: 2.33 (0.27), residues: 370 sheet: 0.74 (0.34), residues: 271 loop : -0.12 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 131 HIS 0.003 0.001 HIS B 183 PHE 0.011 0.001 PHE B 253 TYR 0.012 0.001 TYR A 204 ARG 0.013 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8543 (tptp) cc_final: 0.8075 (tmtt) REVERT: B 175 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: E 19 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8786 (tttm) REVERT: E 51 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8432 (tp) REVERT: E 118 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7157 (p) REVERT: E 160 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7840 (mtp85) REVERT: E 201 ASP cc_start: 0.8048 (p0) cc_final: 0.7685 (t70) REVERT: R 36 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (mm) REVERT: R 137 HIS cc_start: 0.8041 (t-90) cc_final: 0.7796 (t-90) REVERT: R 170 CYS cc_start: 0.7708 (OUTLIER) cc_final: 0.6878 (m) REVERT: R 240 TYR cc_start: 0.8281 (t80) cc_final: 0.7965 (t80) outliers start: 34 outliers final: 17 residues processed: 138 average time/residue: 1.1544 time to fit residues: 170.8478 Evaluate side-chains 137 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 36 ASN B 75 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8855 Z= 0.145 Angle : 0.524 8.867 12042 Z= 0.266 Chirality : 0.040 0.138 1356 Planarity : 0.004 0.053 1543 Dihedral : 4.706 68.462 1249 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.10 % Allowed : 18.94 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.40 (0.26), residues: 1118 helix: 2.40 (0.27), residues: 370 sheet: 0.73 (0.34), residues: 271 loop : -0.08 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.002 0.001 HIS B 183 PHE 0.010 0.001 PHE B 253 TYR 0.010 0.001 TYR A 204 ARG 0.009 0.000 ARG R 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8475 (tptp) cc_final: 0.7939 (tmtt) REVERT: E 51 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8380 (tp) REVERT: E 118 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7138 (p) REVERT: E 160 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7778 (mtp85) REVERT: E 201 ASP cc_start: 0.8039 (p0) cc_final: 0.7666 (t70) REVERT: R 137 HIS cc_start: 0.8010 (t-90) cc_final: 0.7777 (t-90) REVERT: R 170 CYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6757 (m) REVERT: R 240 TYR cc_start: 0.8386 (t80) cc_final: 0.8059 (t80) outliers start: 28 outliers final: 12 residues processed: 137 average time/residue: 1.0830 time to fit residues: 159.4620 Evaluate side-chains 126 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 36 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8855 Z= 0.203 Angle : 0.569 9.352 12042 Z= 0.286 Chirality : 0.041 0.137 1356 Planarity : 0.004 0.052 1543 Dihedral : 4.869 71.389 1249 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.21 % Allowed : 20.16 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.33 (0.26), residues: 1118 helix: 2.25 (0.27), residues: 373 sheet: 0.78 (0.34), residues: 272 loop : -0.11 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 131 HIS 0.004 0.001 HIS B 183 PHE 0.012 0.001 PHE B 253 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG R 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8541 (tptp) cc_final: 0.8054 (tmtt) REVERT: B 15 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7990 (mtmm) REVERT: E 51 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8445 (tp) REVERT: E 118 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7320 (p) REVERT: E 160 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7827 (mtp85) REVERT: E 201 ASP cc_start: 0.8058 (p0) cc_final: 0.7680 (t70) REVERT: E 218 ARG cc_start: 0.7047 (mpp80) cc_final: 0.6821 (mpp80) REVERT: R 137 HIS cc_start: 0.8010 (t-90) cc_final: 0.7786 (t-90) REVERT: R 170 CYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6967 (m) REVERT: R 240 TYR cc_start: 0.8415 (t80) cc_final: 0.8110 (t80) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 1.1351 time to fit residues: 160.4692 Evaluate side-chains 129 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 36 ASN B 75 GLN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8855 Z= 0.180 Angle : 0.559 9.427 12042 Z= 0.283 Chirality : 0.041 0.139 1356 Planarity : 0.004 0.052 1543 Dihedral : 4.879 73.734 1249 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 20.38 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.31 (0.26), residues: 1118 helix: 2.25 (0.27), residues: 373 sheet: 0.71 (0.34), residues: 274 loop : -0.10 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 131 HIS 0.004 0.001 HIS B 183 PHE 0.011 0.001 PHE B 253 TYR 0.010 0.001 TYR R 202 ARG 0.009 0.000 ARG R 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.8531 (tptp) cc_final: 0.8032 (tmtt) REVERT: E 51 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8445 (tp) REVERT: E 118 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7308 (p) REVERT: E 160 ARG cc_start: 0.8049 (ttm110) cc_final: 0.7827 (mtp85) REVERT: E 201 ASP cc_start: 0.8055 (p0) cc_final: 0.7675 (t70) REVERT: E 218 ARG cc_start: 0.7039 (mpp80) cc_final: 0.6807 (mpp80) REVERT: R 137 HIS cc_start: 0.8032 (t-90) cc_final: 0.7762 (t-90) REVERT: R 170 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6846 (m) REVERT: R 240 TYR cc_start: 0.8427 (t80) cc_final: 0.8129 (t80) outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 1.1268 time to fit residues: 155.2698 Evaluate side-chains 132 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 36 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8855 Z= 0.254 Angle : 0.592 9.642 12042 Z= 0.303 Chirality : 0.042 0.136 1356 Planarity : 0.004 0.051 1543 Dihedral : 5.119 76.030 1249 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.33 % Allowed : 20.71 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.26), residues: 1118 helix: 2.05 (0.27), residues: 378 sheet: 0.66 (0.33), residues: 287 loop : -0.13 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.012 0.001 PHE B 253 TYR 0.013 0.002 TYR E 190 ARG 0.009 0.000 ARG R 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 51 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8548 (tp) REVERT: E 118 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7434 (p) REVERT: E 160 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7838 (mtp85) REVERT: E 201 ASP cc_start: 0.8077 (p0) cc_final: 0.7492 (OUTLIER) REVERT: E 218 ARG cc_start: 0.7066 (mpp80) cc_final: 0.6825 (mpp80) REVERT: R 240 TYR cc_start: 0.8501 (t80) cc_final: 0.8182 (t80) outliers start: 21 outliers final: 20 residues processed: 127 average time/residue: 1.0815 time to fit residues: 147.4632 Evaluate side-chains 133 residues out of total 935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN B 36 ASN ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.083583 restraints weight = 15880.623| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.54 r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8855 Z= 0.250 Angle : 0.596 10.088 12042 Z= 0.304 Chirality : 0.042 0.135 1356 Planarity : 0.004 0.051 1543 Dihedral : 5.156 77.148 1249 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.66 % Allowed : 20.38 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1118 helix: 1.99 (0.27), residues: 378 sheet: 0.67 (0.33), residues: 286 loop : -0.17 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 131 HIS 0.006 0.001 HIS B 183 PHE 0.010 0.001 PHE B 180 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG R 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.72 seconds wall clock time: 62 minutes 10.31 seconds (3730.31 seconds total)