Starting phenix.real_space_refine on Wed Feb 14 05:08:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihi_35445/02_2024/8ihi_35445_updated.pdb" } resolution = 3.11 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= 0.077 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 57 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "S PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R PHE 38": "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: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1695 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "S" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1706 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2477 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "R" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'P9X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.71, per 1000 atoms: 0.66 Number of scatterers: 8665 At special positions: 0 Unit cell: (89.1, 117.81, 135.63, 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 57 16.00 O 1591 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.86 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 16 sheets defined 33.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.517A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.293A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.726A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.523A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.545A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.581A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'R' and resid 24 through 54 removed outlier: 3.621A pdb=" N VAL R 29 " --> pdb=" O ILE R 26 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU R 30 " --> pdb=" O VAL R 27 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.845A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU R 37 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 38 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE R 39 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE R 40 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU R 42 " --> pdb=" O ILE R 39 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN R 45 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY R 46 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU R 47 " --> pdb=" O GLY R 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE R 51 " --> pdb=" O ALA R 48 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE R 54 " --> pdb=" O ILE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 88 removed outlier: 3.548A pdb=" N ILE R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU R 80 " --> pdb=" O LEU R 76 " (cutoff:3.500A) Proline residue: R 81 - end of helix removed outlier: 3.529A pdb=" N ASN R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 127 removed outlier: 3.863A pdb=" N LEU R 107 " --> pdb=" O MET R 103 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG R 111 " --> pdb=" O LEU R 107 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 162 No H-bonds generated for 'chain 'R' and resid 160 through 162' Processing helix chain 'R' and resid 188 through 217 removed outlier: 4.064A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.536A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 294 removed outlier: 3.615A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.470A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= C, first strand: chain 'S' and resid 33 through 35 removed outlier: 3.538A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.582A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= F, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= G, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.305A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.991A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.941A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.905A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.789A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.553A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.365A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'R' and resid 10 through 12 Processing sheet with id= P, first strand: chain 'R' and resid 169 through 171 removed outlier: 3.584A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 3.49 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: 2784 1.34 - 1.46: 2206 1.46 - 1.58: 3792 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8861 Sorted by residual: bond pdb=" C1 P9X R 602 " pdb=" C6 P9X R 602 " ideal model delta sigma weight residual 1.402 1.526 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C1 P9X R 602 " pdb=" O1 P9X R 602 " ideal model delta sigma weight residual 1.578 1.462 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C3 P9X R 602 " pdb=" C4 P9X R 602 " ideal model delta sigma weight residual 1.414 1.360 0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C4 P9X R 602 " pdb=" O1 P9X R 602 " ideal model delta sigma weight residual 1.413 1.362 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C4 P9X R 602 " pdb=" C5 P9X R 602 " ideal model delta sigma weight residual 1.527 1.476 0.051 2.00e-02 2.50e+03 6.55e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.84: 187 106.84 - 113.62: 4891 113.62 - 120.41: 3262 120.41 - 127.20: 3598 127.20 - 133.99: 100 Bond angle restraints: 12038 Sorted by residual: angle pdb=" C3 P9X R 602 " pdb=" C4 P9X R 602 " pdb=" C5 P9X R 602 " ideal model delta sigma weight residual 120.00 132.00 -12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET R 167 " pdb=" CG MET R 167 " pdb=" SD MET R 167 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA PRO S 151 " pdb=" N PRO S 151 " pdb=" CD PRO S 151 " ideal model delta sigma weight residual 112.00 107.01 4.99 1.40e+00 5.10e-01 1.27e+01 angle pdb=" C ASP R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.73e+00 angle pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sigma weight residual 116.30 125.82 -9.52 3.50e+00 8.16e-02 7.41e+00 ... (remaining 12033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4481 17.92 - 35.84: 543 35.84 - 53.77: 135 53.77 - 71.69: 29 71.69 - 89.61: 5 Dihedral angle restraints: 5193 sinusoidal: 1917 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -138.25 52.25 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual -86.00 -55.41 -30.59 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 804 0.027 - 0.054: 360 0.054 - 0.081: 121 0.081 - 0.108: 67 0.108 - 0.134: 26 Chirality restraints: 1378 Sorted by residual: chirality pdb=" C1 P9X R 602 " pdb=" C2 P9X R 602 " pdb=" C6 P9X R 602 " pdb=" O1 P9X R 602 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL S 147 " pdb=" N VAL S 147 " pdb=" C VAL S 147 " pdb=" CB VAL S 147 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASP S 90 " pdb=" N ASP S 90 " pdb=" C ASP S 90 " pdb=" CB ASP S 90 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1375 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO S 151 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO R 32 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO C 53 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.027 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1386 2.76 - 3.29: 7991 3.29 - 3.83: 13828 3.83 - 4.36: 16937 4.36 - 4.90: 29916 Nonbonded interactions: 70058 Sorted by model distance: nonbonded pdb=" O LEU R 280 " pdb=" OG1 THR R 283 " model vdw 2.221 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.239 2.440 nonbonded pdb=" O GLY R 262 " pdb=" OH TYR R 269 " model vdw 2.255 2.440 nonbonded pdb=" O LEU R 257 " pdb=" OG SER R 261 " model vdw 2.264 2.440 ... (remaining 70053 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: 1.500 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: 0.020 Extract box with map and model: 6.950 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.003 0.124 8861 Z= 0.239 Angle : 0.547 12.002 12038 Z= 0.276 Chirality : 0.040 0.134 1378 Planarity : 0.005 0.122 1522 Dihedral : 16.762 89.608 3063 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.22 % Allowed : 25.98 % Favored : 73.80 % 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: -0.60 (0.25), residues: 1115 helix: 0.14 (0.28), residues: 352 sheet: -0.02 (0.31), residues: 269 loop : -0.92 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 152 HIS 0.002 0.000 HIS R 189 PHE 0.026 0.001 PHE R 38 TYR 0.021 0.001 TYR S 235 ARG 0.005 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: S 69 THR cc_start: 0.8404 (t) cc_final: 0.8071 (m) REVERT: S 87 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7526 (mtm-85) REVERT: C 42 GLU cc_start: 0.7684 (mp0) cc_final: 0.7262 (mp0) outliers start: 2 outliers final: 2 residues processed: 145 average time/residue: 0.2192 time to fit residues: 43.7485 Evaluate side-chains 136 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.0060 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8861 Z= 0.262 Angle : 0.551 6.873 12038 Z= 0.286 Chirality : 0.042 0.169 1378 Planarity : 0.005 0.083 1522 Dihedral : 5.223 57.589 1240 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.46 % Allowed : 24.75 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.21 (0.25), residues: 1115 helix: 0.98 (0.27), residues: 359 sheet: 0.04 (0.32), residues: 258 loop : -1.03 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.002 PHE R 232 TYR 0.022 0.001 TYR S 235 ARG 0.005 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.004 Fit side-chains REVERT: A 197 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8314 (mtmt) REVERT: A 281 SER cc_start: 0.8026 (m) cc_final: 0.7818 (t) REVERT: S 67 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6753 (mtm110) REVERT: B 234 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8744 (m-80) outliers start: 31 outliers final: 15 residues processed: 157 average time/residue: 0.2161 time to fit residues: 46.3455 Evaluate side-chains 140 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 80 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8861 Z= 0.160 Angle : 0.492 10.315 12038 Z= 0.252 Chirality : 0.041 0.148 1378 Planarity : 0.004 0.066 1522 Dihedral : 4.717 50.034 1237 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.46 % Allowed : 25.98 % Favored : 70.57 % 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: 0.22 (0.25), residues: 1115 helix: 1.71 (0.28), residues: 353 sheet: 0.15 (0.32), residues: 252 loop : -0.97 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.000 HIS A 188 PHE 0.011 0.001 PHE A 354 TYR 0.019 0.001 TYR S 235 ARG 0.003 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.980 Fit side-chains REVERT: A 197 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8449 (mtmt) REVERT: S 67 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6768 (mtm110) REVERT: S 87 ARG cc_start: 0.7719 (mtt180) cc_final: 0.7395 (mtm-85) REVERT: B 124 TYR cc_start: 0.8906 (m-80) cc_final: 0.8561 (m-80) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8739 (m-80) outliers start: 31 outliers final: 14 residues processed: 156 average time/residue: 0.2155 time to fit residues: 45.9477 Evaluate side-chains 140 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8861 Z= 0.155 Angle : 0.482 7.750 12038 Z= 0.246 Chirality : 0.040 0.132 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.329 42.766 1237 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.79 % Allowed : 27.54 % Favored : 69.68 % 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: 0.35 (0.26), residues: 1115 helix: 1.96 (0.28), residues: 352 sheet: 0.14 (0.32), residues: 254 loop : -0.96 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.000 HIS A 188 PHE 0.017 0.001 PHE R 38 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 87 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7521 (mtm-85) REVERT: B 124 TYR cc_start: 0.8914 (m-80) cc_final: 0.8578 (m-80) REVERT: B 234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: C 42 GLU cc_start: 0.7287 (mp0) cc_final: 0.6585 (mp0) REVERT: R 14 ASP cc_start: 0.7105 (m-30) cc_final: 0.6422 (t0) REVERT: R 150 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8074 (tt) REVERT: R 234 MET cc_start: 0.8169 (mmt) cc_final: 0.7929 (mmt) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.2102 time to fit residues: 42.9613 Evaluate side-chains 144 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 284 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8861 Z= 0.150 Angle : 0.477 7.472 12038 Z= 0.244 Chirality : 0.040 0.142 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.072 40.801 1237 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.23 % Allowed : 26.98 % Favored : 69.79 % 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: 0.47 (0.26), residues: 1115 helix: 2.13 (0.28), residues: 352 sheet: 0.20 (0.32), residues: 254 loop : -0.95 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.022 0.001 PHE R 38 TYR 0.017 0.001 TYR S 235 ARG 0.002 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.072 Fit side-chains REVERT: A 197 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8426 (mtmt) REVERT: S 67 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6785 (mtm110) REVERT: S 87 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7195 (mtm-85) REVERT: B 124 TYR cc_start: 0.8922 (m-80) cc_final: 0.8534 (m-80) REVERT: B 234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: C 42 GLU cc_start: 0.7239 (mp0) cc_final: 0.6536 (mp0) REVERT: R 14 ASP cc_start: 0.7104 (m-30) cc_final: 0.6588 (t0) outliers start: 29 outliers final: 22 residues processed: 152 average time/residue: 0.2181 time to fit residues: 45.8482 Evaluate side-chains 153 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 188 HIS S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8861 Z= 0.171 Angle : 0.493 10.669 12038 Z= 0.249 Chirality : 0.040 0.145 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.060 39.222 1237 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.79 % Allowed : 26.76 % Favored : 69.45 % 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: 0.48 (0.26), residues: 1115 helix: 2.16 (0.28), residues: 352 sheet: 0.20 (0.32), residues: 254 loop : -0.95 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.022 0.001 PHE R 38 TYR 0.018 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.420 Fit side-chains REVERT: S 67 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6815 (mtm110) REVERT: S 87 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7268 (mtm-85) REVERT: B 124 TYR cc_start: 0.8967 (m-80) cc_final: 0.8630 (m-80) REVERT: B 234 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: C 42 GLU cc_start: 0.7236 (mp0) cc_final: 0.6531 (mp0) REVERT: R 14 ASP cc_start: 0.7502 (m-30) cc_final: 0.6950 (t0) outliers start: 34 outliers final: 27 residues processed: 156 average time/residue: 0.2346 time to fit residues: 50.9773 Evaluate side-chains 158 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- 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 255 ASN S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8861 Z= 0.218 Angle : 0.511 8.683 12038 Z= 0.259 Chirality : 0.041 0.138 1378 Planarity : 0.004 0.058 1522 Dihedral : 4.166 37.808 1237 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.12 % Allowed : 27.09 % Favored : 68.78 % 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: 0.46 (0.26), residues: 1115 helix: 2.17 (0.29), residues: 350 sheet: 0.11 (0.32), residues: 261 loop : -0.93 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.000 HIS B 91 PHE 0.019 0.001 PHE R 38 TYR 0.018 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.041 Fit side-chains REVERT: A 197 LYS cc_start: 0.8522 (mttm) cc_final: 0.8306 (mmtt) REVERT: S 67 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6744 (mtm110) REVERT: B 124 TYR cc_start: 0.9007 (m-80) cc_final: 0.8723 (m-80) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8795 (m-80) REVERT: C 42 GLU cc_start: 0.7238 (mp0) cc_final: 0.6491 (mp0) REVERT: R 14 ASP cc_start: 0.7580 (m-30) cc_final: 0.7116 (t0) REVERT: R 165 LYS cc_start: 0.7006 (mmmt) cc_final: 0.6797 (mmtt) outliers start: 37 outliers final: 29 residues processed: 162 average time/residue: 0.2121 time to fit residues: 47.4685 Evaluate side-chains 162 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8861 Z= 0.191 Angle : 0.515 12.283 12038 Z= 0.259 Chirality : 0.041 0.147 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.107 33.984 1237 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.23 % Allowed : 27.98 % Favored : 68.78 % 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: 0.56 (0.26), residues: 1115 helix: 2.20 (0.29), residues: 351 sheet: 0.25 (0.32), residues: 261 loop : -0.90 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.024 0.001 PHE R 38 TYR 0.021 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.942 Fit side-chains REVERT: A 197 LYS cc_start: 0.8541 (mttm) cc_final: 0.8326 (mmtt) REVERT: S 18 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6194 (tpt90) REVERT: S 67 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7649 (mtm180) REVERT: S 87 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7426 (mtm-85) REVERT: B 124 TYR cc_start: 0.8991 (m-80) cc_final: 0.8705 (m-80) REVERT: B 234 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8784 (m-80) REVERT: C 42 GLU cc_start: 0.7226 (mp0) cc_final: 0.6479 (mp0) REVERT: R 14 ASP cc_start: 0.7567 (m-30) cc_final: 0.6976 (t0) REVERT: R 165 LYS cc_start: 0.7018 (mmmt) cc_final: 0.5870 (mttt) outliers start: 29 outliers final: 23 residues processed: 153 average time/residue: 0.2246 time to fit residues: 46.2102 Evaluate side-chains 155 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8861 Z= 0.240 Angle : 0.534 9.542 12038 Z= 0.271 Chirality : 0.042 0.158 1378 Planarity : 0.004 0.058 1522 Dihedral : 4.207 33.953 1237 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.90 % Allowed : 27.31 % Favored : 68.78 % 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: 0.50 (0.26), residues: 1115 helix: 2.10 (0.29), residues: 351 sheet: 0.19 (0.32), residues: 262 loop : -0.88 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.001 PHE R 38 TYR 0.022 0.001 TYR S 235 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 87 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7474 (mtm-85) REVERT: B 124 TYR cc_start: 0.9017 (m-80) cc_final: 0.8779 (m-80) REVERT: B 234 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: C 42 GLU cc_start: 0.7231 (mp0) cc_final: 0.6473 (mp0) REVERT: R 14 ASP cc_start: 0.7585 (m-30) cc_final: 0.6972 (t0) REVERT: R 165 LYS cc_start: 0.7089 (mmmt) cc_final: 0.5961 (mttt) outliers start: 35 outliers final: 27 residues processed: 158 average time/residue: 0.2149 time to fit residues: 46.8256 Evaluate side-chains 156 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 171 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 306 GLN A 322 HIS S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8861 Z= 0.155 Angle : 0.508 10.407 12038 Z= 0.254 Chirality : 0.040 0.137 1378 Planarity : 0.004 0.057 1522 Dihedral : 4.033 32.853 1237 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.79 % Allowed : 28.76 % Favored : 68.45 % 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: 0.63 (0.26), residues: 1115 helix: 2.29 (0.29), residues: 351 sheet: 0.30 (0.32), residues: 256 loop : -0.88 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.002 0.000 HIS B 91 PHE 0.024 0.001 PHE R 38 TYR 0.020 0.001 TYR S 235 ARG 0.003 0.000 ARG R 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8537 (mttm) cc_final: 0.8319 (mmtt) REVERT: S 87 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7268 (mtm-85) REVERT: B 124 TYR cc_start: 0.8966 (m-80) cc_final: 0.8642 (m-80) REVERT: B 234 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8762 (m-80) REVERT: C 42 GLU cc_start: 0.7210 (mp0) cc_final: 0.6467 (mp0) REVERT: R 14 ASP cc_start: 0.7524 (m-30) cc_final: 0.6952 (t0) REVERT: R 165 LYS cc_start: 0.7073 (mmmt) cc_final: 0.5945 (mttt) outliers start: 25 outliers final: 22 residues processed: 150 average time/residue: 0.2051 time to fit residues: 42.6373 Evaluate side-chains 154 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 217 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 268 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117632 restraints weight = 11372.957| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.49 r_work: 0.3329 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8861 Z= 0.246 Angle : 0.542 10.645 12038 Z= 0.273 Chirality : 0.042 0.159 1378 Planarity : 0.004 0.058 1522 Dihedral : 4.182 32.629 1237 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.12 % Allowed : 28.32 % Favored : 68.56 % 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: 0.52 (0.26), residues: 1115 helix: 2.14 (0.29), residues: 351 sheet: 0.20 (0.32), residues: 262 loop : -0.88 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.002 PHE R 38 TYR 0.022 0.001 TYR S 235 ARG 0.004 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.70 seconds wall clock time: 41 minutes 44.89 seconds (2504.89 seconds total)