Starting phenix.real_space_refine on Mon Mar 11 17:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuy_32131/03_2024/7vuy_32131_updated.pdb" } resolution = 2.84 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= 0.005 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 65 5.16 5 C 5572 2.51 5 N 1458 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 126": "OE1" <-> "OE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 143": "NH1" <-> "NH2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 252": "OD1" <-> "OD2" Residue "R PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.56 Number of scatterers: 8708 At special positions: 0 Unit cell: (116.833, 107.718, 105.232, 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 65 16.00 O 1613 8.00 N 1458 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 34.4% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'R' and resid 31 through 57 Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.646A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 177 through 212 removed outlier: 4.205A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 244 removed outlier: 4.601A pdb=" N LEU R 237 " --> pdb=" O LEU R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 253 through 279 removed outlier: 4.162A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 281 through 284 No H-bonds generated for 'chain 'R' and resid 281 through 284' Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.984A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) 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 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.984A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 22 Processing helix chain 'G' and resid 30 through 43 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 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.522A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.990A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 166 through 168 Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.538A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.858A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.852A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.556A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.847A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.618A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.762A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.964A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'S' and resid 217 through 219 removed outlier: 6.249A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1110 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: 2.75 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2778 1.34 - 1.47: 2334 1.47 - 1.61: 3696 1.61 - 1.74: 1 1.74 - 1.87: 90 Bond restraints: 8899 Sorted by residual: bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.34e-02 1.83e+03 7.52e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.41e-02 5.03e+03 1.93e+01 bond pdb=" N ILE R 260 " pdb=" CA ILE R 260 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N ILE R 249 " pdb=" CA ILE R 249 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 ... (remaining 8894 not shown) Histogram of bond angle deviations from ideal: 95.73 - 103.45: 80 103.45 - 111.18: 3354 111.18 - 118.90: 3781 118.90 - 126.63: 4718 126.63 - 134.35: 130 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.93 129.44 -8.51 1.06e+00 8.90e-01 6.45e+01 angle pdb=" O HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.71 113.17 7.54 9.40e-01 1.13e+00 6.44e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.12 -12.72 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 113.43 120.34 -6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" O GLN R 242 " pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 122.15 116.44 5.71 1.14e+00 7.69e-01 2.51e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4744 17.09 - 34.18: 453 34.18 - 51.27: 74 51.27 - 68.36: 12 68.36 - 85.45: 9 Dihedral angle restraints: 5292 sinusoidal: 2084 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1119 0.082 - 0.163: 220 0.163 - 0.245: 25 0.245 - 0.327: 4 0.327 - 0.408: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1369 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 261 " -0.045 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO R 262 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO S 41 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO G 55 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.038 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 31 2.42 - 3.04: 4917 3.04 - 3.66: 13380 3.66 - 4.28: 20079 4.28 - 4.90: 34041 Nonbonded interactions: 72448 Sorted by model distance: nonbonded pdb=" OE1 GLN R 181 " pdb=" CD1 TRP R 248 " model vdw 1.806 3.260 nonbonded pdb=" OE1 GLN R 181 " pdb=" NE1 TRP R 248 " model vdw 2.141 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.223 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 2.440 ... (remaining 72443 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.320 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.010 0.203 8899 Z= 0.609 Angle : 1.119 12.716 12063 Z= 0.608 Chirality : 0.068 0.408 1372 Planarity : 0.007 0.073 1514 Dihedral : 13.835 85.451 3212 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.42 % Allowed : 0.95 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.74 (0.23), residues: 1098 helix: -0.35 (0.24), residues: 367 sheet: -1.40 (0.29), residues: 285 loop : -1.50 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.017 0.002 HIS A 213 PHE 0.027 0.003 PHE R 183 TYR 0.027 0.003 TYR R 113 ARG 0.022 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7986 (mpp) cc_final: 0.7597 (mmt) REVERT: A 305 CYS cc_start: 0.7550 (m) cc_final: 0.7299 (m) REVERT: B 6 GLN cc_start: 0.7374 (pp30) cc_final: 0.7009 (pp30) REVERT: B 15 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7922 (mmmt) REVERT: B 290 ASP cc_start: 0.7987 (m-30) cc_final: 0.7759 (m-30) outliers start: 4 outliers final: 2 residues processed: 177 average time/residue: 1.3088 time to fit residues: 245.2961 Evaluate side-chains 129 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS A 52 GLN A 188 HIS A 306 GLN A 322 HIS A 331 ASN B 340 ASN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8899 Z= 0.231 Angle : 0.618 7.495 12063 Z= 0.319 Chirality : 0.043 0.258 1372 Planarity : 0.004 0.051 1514 Dihedral : 6.887 77.485 1267 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.11 % Allowed : 14.23 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.86 (0.25), residues: 1098 helix: 0.89 (0.26), residues: 369 sheet: -1.29 (0.29), residues: 278 loop : -1.23 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.016 0.001 PHE R 183 TYR 0.020 0.002 TYR R 113 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: R 208 ARG cc_start: 0.7429 (tpt-90) cc_final: 0.7062 (tpt90) REVERT: R 220 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.6950 (ttt-90) REVERT: R 257 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4878 (t80) REVERT: A 51 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7677 (mmtt) REVERT: A 305 CYS cc_start: 0.7730 (m) cc_final: 0.7303 (m) REVERT: B 6 GLN cc_start: 0.7274 (pp30) cc_final: 0.6850 (pp30) REVERT: S 148 ARG cc_start: 0.7655 (mtp85) cc_final: 0.7418 (mtp85) outliers start: 20 outliers final: 11 residues processed: 162 average time/residue: 1.1018 time to fit residues: 191.7417 Evaluate side-chains 147 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8899 Z= 0.285 Angle : 0.616 8.868 12063 Z= 0.315 Chirality : 0.044 0.226 1372 Planarity : 0.004 0.044 1514 Dihedral : 6.380 79.236 1263 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.69 % Allowed : 16.65 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1098 helix: 1.38 (0.26), residues: 366 sheet: -1.33 (0.29), residues: 272 loop : -1.19 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.023 0.001 PHE R 94 TYR 0.020 0.002 TYR R 113 ARG 0.004 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.7056 (ttt-90) REVERT: R 257 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.4851 (t80) REVERT: A 25 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 51 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7777 (mmtt) REVERT: A 305 CYS cc_start: 0.7742 (m) cc_final: 0.7311 (m) REVERT: A 349 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7970 (tmmt) REVERT: B 6 GLN cc_start: 0.7277 (pp30) cc_final: 0.6840 (pp30) REVERT: S 148 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7487 (mtp85) outliers start: 35 outliers final: 15 residues processed: 173 average time/residue: 1.0940 time to fit residues: 202.6300 Evaluate side-chains 159 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 306 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8899 Z= 0.280 Angle : 0.608 8.716 12063 Z= 0.311 Chirality : 0.044 0.176 1372 Planarity : 0.003 0.041 1514 Dihedral : 5.941 79.934 1263 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.95 % Allowed : 16.23 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.45 (0.25), residues: 1098 helix: 1.60 (0.27), residues: 367 sheet: -1.32 (0.29), residues: 275 loop : -1.17 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.019 0.001 PHE R 94 TYR 0.021 0.002 TYR R 113 ARG 0.004 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 156 time to evaluate : 0.999 Fit side-chains REVERT: R 220 ARG cc_start: 0.7447 (ttm-80) cc_final: 0.7009 (ttt-90) REVERT: R 226 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (mm) REVERT: R 257 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.4833 (t80) REVERT: A 51 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7802 (mmtt) REVERT: A 193 ASP cc_start: 0.7450 (m-30) cc_final: 0.7027 (t0) REVERT: A 240 MET cc_start: 0.6598 (mmm) cc_final: 0.6170 (mmt) REVERT: A 305 CYS cc_start: 0.7738 (m) cc_final: 0.7331 (m) REVERT: A 349 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7990 (tmmt) REVERT: B 6 GLN cc_start: 0.7215 (pp30) cc_final: 0.6773 (pp30) REVERT: B 35 ASN cc_start: 0.8318 (t0) cc_final: 0.7938 (p0) REVERT: B 37 ILE cc_start: 0.7904 (tt) cc_final: 0.7670 (pt) REVERT: S 148 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7435 (mtp85) outliers start: 47 outliers final: 24 residues processed: 184 average time/residue: 1.0904 time to fit residues: 214.8123 Evaluate side-chains 175 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8899 Z= 0.275 Angle : 0.612 9.593 12063 Z= 0.309 Chirality : 0.043 0.178 1372 Planarity : 0.003 0.039 1514 Dihedral : 5.801 80.158 1263 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.64 % Allowed : 18.55 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.38 (0.25), residues: 1098 helix: 1.71 (0.27), residues: 368 sheet: -1.35 (0.29), residues: 277 loop : -1.12 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE R 94 TYR 0.021 0.002 TYR R 113 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 1.028 Fit side-chains REVERT: R 226 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7699 (mm) REVERT: A 25 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: A 51 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7788 (mmtt) REVERT: A 193 ASP cc_start: 0.7463 (m-30) cc_final: 0.7017 (t0) REVERT: A 305 CYS cc_start: 0.7738 (m) cc_final: 0.7327 (m) REVERT: A 349 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7999 (tmmt) REVERT: B 6 GLN cc_start: 0.7187 (pp30) cc_final: 0.6754 (pp30) REVERT: S 148 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7448 (mtp85) outliers start: 44 outliers final: 24 residues processed: 177 average time/residue: 1.1118 time to fit residues: 210.7797 Evaluate side-chains 173 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 0.0570 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8899 Z= 0.149 Angle : 0.569 10.446 12063 Z= 0.281 Chirality : 0.041 0.172 1372 Planarity : 0.003 0.037 1514 Dihedral : 5.386 79.748 1263 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.06 % Allowed : 21.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.10 (0.26), residues: 1098 helix: 1.99 (0.27), residues: 369 sheet: -1.31 (0.29), residues: 276 loop : -0.91 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.013 0.001 PHE R 94 TYR 0.023 0.001 TYR R 113 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 0.965 Fit side-chains REVERT: R 220 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.7094 (ttt-90) REVERT: R 226 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7671 (mm) REVERT: A 51 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7723 (mmtt) REVERT: A 193 ASP cc_start: 0.7433 (m-30) cc_final: 0.6988 (t0) REVERT: A 305 CYS cc_start: 0.7849 (m) cc_final: 0.7411 (m) REVERT: B 6 GLN cc_start: 0.7199 (pp30) cc_final: 0.6751 (pp30) REVERT: B 35 ASN cc_start: 0.8309 (t0) cc_final: 0.7933 (p0) REVERT: B 262 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7321 (mtt) outliers start: 29 outliers final: 13 residues processed: 180 average time/residue: 1.1014 time to fit residues: 212.4905 Evaluate side-chains 157 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 0.0570 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8899 Z= 0.146 Angle : 0.566 11.154 12063 Z= 0.280 Chirality : 0.041 0.173 1372 Planarity : 0.003 0.036 1514 Dihedral : 5.257 80.792 1263 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.63 % Allowed : 23.50 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.07 (0.26), residues: 1098 helix: 2.19 (0.27), residues: 370 sheet: -1.24 (0.30), residues: 278 loop : -0.85 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.020 0.001 TYR R 113 ARG 0.007 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.016 Fit side-chains REVERT: R 226 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 25 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 193 ASP cc_start: 0.7422 (m-30) cc_final: 0.6951 (t0) REVERT: A 280 LYS cc_start: 0.8622 (tmmm) cc_final: 0.8205 (tppt) REVERT: A 282 PRO cc_start: 0.7456 (Cg_endo) cc_final: 0.7208 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7771 (m) cc_final: 0.7321 (m) REVERT: B 6 GLN cc_start: 0.7127 (pp30) cc_final: 0.6692 (pp30) REVERT: B 17 GLN cc_start: 0.8201 (tt0) cc_final: 0.7912 (tp-100) REVERT: B 35 ASN cc_start: 0.8257 (t0) cc_final: 0.7928 (p0) REVERT: B 234 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7898 (m-80) outliers start: 25 outliers final: 12 residues processed: 170 average time/residue: 1.0745 time to fit residues: 196.0902 Evaluate side-chains 149 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS A 188 HIS B 13 GLN B 44 GLN S 39 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8899 Z= 0.159 Angle : 0.585 11.361 12063 Z= 0.286 Chirality : 0.041 0.174 1372 Planarity : 0.003 0.049 1514 Dihedral : 5.244 80.977 1263 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.63 % Allowed : 24.24 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.12 (0.26), residues: 1098 helix: 2.13 (0.27), residues: 376 sheet: -1.20 (0.30), residues: 273 loop : -0.80 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.019 0.001 TYR R 113 ARG 0.013 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.968 Fit side-chains REVERT: R 226 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7602 (mm) REVERT: A 25 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 51 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7818 (mmtt) REVERT: A 193 ASP cc_start: 0.7423 (m-30) cc_final: 0.6922 (t0) REVERT: A 280 LYS cc_start: 0.8632 (tmmm) cc_final: 0.8227 (tppt) REVERT: A 282 PRO cc_start: 0.7446 (Cg_endo) cc_final: 0.7229 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7804 (m) cc_final: 0.7342 (m) REVERT: B 6 GLN cc_start: 0.7105 (pp30) cc_final: 0.6680 (pp30) REVERT: B 35 ASN cc_start: 0.8274 (t0) cc_final: 0.7937 (p0) REVERT: B 46 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7349 (mmm-85) REVERT: B 234 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7890 (m-80) outliers start: 25 outliers final: 13 residues processed: 162 average time/residue: 1.0892 time to fit residues: 189.2107 Evaluate side-chains 157 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS A 188 HIS B 13 GLN B 44 GLN S 39 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8899 Z= 0.383 Angle : 0.708 11.808 12063 Z= 0.352 Chirality : 0.046 0.185 1372 Planarity : 0.004 0.045 1514 Dihedral : 5.812 81.801 1263 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.37 % Allowed : 24.34 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.24 (0.26), residues: 1098 helix: 1.80 (0.26), residues: 373 sheet: -1.28 (0.29), residues: 275 loop : -1.03 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 248 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.002 PHE B 234 TYR 0.018 0.002 TYR R 113 ARG 0.012 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.060 Fit side-chains REVERT: R 226 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 193 ASP cc_start: 0.7509 (m-30) cc_final: 0.7293 (m-30) REVERT: A 280 LYS cc_start: 0.8623 (tmmm) cc_final: 0.8227 (tppt) REVERT: A 305 CYS cc_start: 0.7852 (m) cc_final: 0.7411 (m) REVERT: B 6 GLN cc_start: 0.7150 (pp30) cc_final: 0.6716 (pp30) REVERT: B 35 ASN cc_start: 0.8449 (t0) cc_final: 0.8044 (p0) REVERT: B 46 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7326 (mmm-85) REVERT: B 234 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7896 (m-80) outliers start: 32 outliers final: 16 residues processed: 172 average time/residue: 1.1322 time to fit residues: 208.2027 Evaluate side-chains 159 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 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 188 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 44 GLN S 13 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8899 Z= 0.242 Angle : 0.666 12.059 12063 Z= 0.326 Chirality : 0.043 0.177 1372 Planarity : 0.004 0.051 1514 Dihedral : 5.615 81.231 1263 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.21 % Allowed : 25.71 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.17 (0.26), residues: 1098 helix: 1.83 (0.26), residues: 375 sheet: -1.26 (0.30), residues: 273 loop : -0.97 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.022 0.002 TYR R 113 ARG 0.013 0.001 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 0.921 Fit side-chains REVERT: R 226 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7712 (mm) REVERT: A 51 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7556 (mtmt) REVERT: A 193 ASP cc_start: 0.7470 (m-30) cc_final: 0.6941 (t0) REVERT: A 280 LYS cc_start: 0.8629 (tmmm) cc_final: 0.8236 (tppt) REVERT: A 305 CYS cc_start: 0.7835 (m) cc_final: 0.7396 (m) REVERT: B 6 GLN cc_start: 0.7089 (pp30) cc_final: 0.6668 (pp30) REVERT: B 35 ASN cc_start: 0.8426 (t0) cc_final: 0.8053 (p0) REVERT: B 46 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7335 (mmm-85) REVERT: B 234 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7897 (m-80) outliers start: 21 outliers final: 17 residues processed: 157 average time/residue: 1.1111 time to fit residues: 186.6366 Evaluate side-chains 159 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 44 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139143 restraints weight = 10938.687| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.48 r_work: 0.3694 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8899 Z= 0.190 Angle : 0.648 13.225 12063 Z= 0.314 Chirality : 0.042 0.175 1372 Planarity : 0.003 0.051 1514 Dihedral : 5.393 80.712 1263 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.32 % Allowed : 25.71 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.03 (0.26), residues: 1098 helix: 2.04 (0.27), residues: 370 sheet: -1.23 (0.30), residues: 278 loop : -0.79 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.023 0.001 TYR R 113 ARG 0.013 0.001 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.08 seconds wall clock time: 68 minutes 33.27 seconds (4113.27 seconds total)