Starting phenix.real_space_refine on Thu Mar 14 16:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbm_22120/03_2024/6xbm_22120_updated.pdb" } resolution = 3.14 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= 0.002 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 64 5.16 5 C 5880 2.51 5 N 1543 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 194": "OE1" <-> "OE2" Residue "R TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 287": "OD1" <-> "OD2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R GLU 310": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Residue "R GLU 447": "OE1" <-> "OE2" Residue "R ASP 473": "OD1" <-> "OD2" Residue "R PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 481": "OE1" <-> "OE2" Residue "R ARG 482": "NH1" <-> "NH2" Residue "R ARG 485": "NH1" <-> "NH2" Residue "R ASP 486": "OD1" <-> "OD2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 189": "OD1" <-> "OD2" Residue "S PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2618 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'CO1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.40, per 1000 atoms: 0.59 Number of scatterers: 9211 At special positions: 0 Unit cell: (105.664, 112.32, 126.464, 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 64 16.00 O 1724 8.00 N 1543 7.00 C 5880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.02 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 14 sheets defined 33.4% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'R' and resid 224 through 255 removed outlier: 4.179A pdb=" N ASP R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 284 removed outlier: 3.693A pdb=" N ILE R 266 " --> pdb=" O TYR R 262 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE R 268 " --> pdb=" O ALA R 264 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 294 Processing helix chain 'R' and resid 313 through 345 removed outlier: 3.557A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 357 through 378 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 397 through 432 Proline residue: R 407 - end of helix removed outlier: 4.262A pdb=" N LYS R 430 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 439 through 495 removed outlier: 4.483A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG R 482 " --> pdb=" O ALA R 478 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG R 485 " --> pdb=" O GLU R 481 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN R 491 " --> pdb=" O TYR R 487 " (cutoff:3.500A) Processing helix chain 'R' and resid 515 through 536 removed outlier: 4.372A pdb=" N TRP R 535 " --> pdb=" O ALA R 531 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL R 536 " --> pdb=" O MET R 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.720A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 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: 4.139A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) 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 308 removed outlier: 3.786A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.770A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (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 sheet with id= A, first strand: chain 'R' and resid 381 through 383 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.568A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 49 through 51 Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.983A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.892A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.645A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.707A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 275 through 278 removed outlier: 5.825A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.612A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.751A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.455A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 143 through 147 419 hydrogen bonds defined for protein. 1197 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: 2.58 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1925 1.33 - 1.45: 2224 1.45 - 1.58: 5160 1.58 - 1.70: 19 1.70 - 1.82: 92 Bond restraints: 9420 Sorted by residual: bond pdb=" C14 CO1 R 702 " pdb=" C7 CO1 R 702 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C14 CO1 R 701 " pdb=" C7 CO1 R 701 " ideal model delta sigma weight residual 1.519 1.626 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.30e-03 1.16e+04 1.77e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.60e-03 1.73e+04 1.75e+01 bond pdb=" C10 CO1 R 701 " pdb=" C17 CO1 R 701 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 56.06 - 71.78: 6 71.78 - 87.49: 0 87.49 - 103.21: 52 103.21 - 118.93: 8575 118.93 - 134.65: 4144 Bond angle restraints: 12777 Sorted by residual: angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.33 125.40 -5.07 8.00e-01 1.56e+00 4.02e+01 angle pdb=" C PHE R 526 " pdb=" N GLY R 527 " pdb=" CA GLY R 527 " ideal model delta sigma weight residual 119.98 124.88 -4.90 1.11e+00 8.12e-01 1.95e+01 angle pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" CA THR R 466 " pdb=" CB THR R 466 " pdb=" OG1 THR R 466 " ideal model delta sigma weight residual 109.60 103.23 6.37 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C THR A 295 " pdb=" N TYR A 296 " pdb=" CA TYR A 296 " ideal model delta sigma weight residual 120.44 125.88 -5.44 1.30e+00 5.92e-01 1.75e+01 ... (remaining 12772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5059 16.81 - 33.62: 457 33.62 - 50.42: 91 50.42 - 67.23: 21 67.23 - 84.04: 9 Dihedral angle restraints: 5637 sinusoidal: 2266 harmonic: 3371 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CB CYS R 193 " pdb=" SG CYS R 193 " pdb=" SG CYS R 213 " pdb=" CB CYS R 213 " ideal model delta sinusoidal sigma weight residual 93.00 172.76 -79.76 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CA GLU R 305 " pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta harmonic sigma weight residual 180.00 140.97 39.03 0 5.00e+00 4.00e-02 6.09e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1037 0.091 - 0.182: 377 0.182 - 0.273: 12 0.273 - 0.364: 1 0.364 - 0.455: 6 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C2 CO1 R 701 " pdb=" C1 CO1 R 701 " pdb=" C5 CO1 R 701 " pdb=" C6 CO1 R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C7 CO1 R 702 " pdb=" C14 CO1 R 702 " pdb=" C15 CO1 R 702 " pdb=" C3 CO1 R 702 " both_signs ideal model delta sigma weight residual False 2.86 3.31 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C2 CO1 R 702 " pdb=" C1 CO1 R 702 " pdb=" C5 CO1 R 702 " pdb=" C6 CO1 R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1430 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA S 199 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ALA S 199 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA S 199 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE S 200 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 262 " -0.020 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR R 262 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR R 262 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 262 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR R 262 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 262 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 262 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.015 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" CG TRP B 99 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 485 2.75 - 3.29: 9218 3.29 - 3.82: 14325 3.82 - 4.36: 18939 4.36 - 4.90: 31773 Nonbonded interactions: 74740 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.211 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 2.440 nonbonded pdb=" O SER S 196 " pdb=" O ALA S 199 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR R 349 " pdb=" O ARG A 32 " model vdw 2.325 2.440 nonbonded pdb=" O GLU R 292 " pdb=" NH2 ARG R 302 " model vdw 2.334 2.520 ... (remaining 74735 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: 0.890 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: 5.220 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 28.430 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.014 0.113 9420 Z= 0.904 Angle : 1.682 9.278 12777 Z= 1.246 Chirality : 0.083 0.455 1433 Planarity : 0.004 0.038 1609 Dihedral : 13.683 84.039 3456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -2.64 (0.22), residues: 1152 helix: -0.79 (0.23), residues: 392 sheet: -2.30 (0.30), residues: 243 loop : -2.15 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 99 HIS 0.008 0.001 HIS B 62 PHE 0.020 0.003 PHE R 285 TYR 0.037 0.003 TYR R 262 ARG 0.003 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8679 (mt0) cc_final: 0.8309 (mp10) REVERT: R 305 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5867 (tm-30) REVERT: R 344 LYS cc_start: 0.8350 (tttt) cc_final: 0.7831 (ttpp) REVERT: R 519 LYS cc_start: 0.8079 (mttt) cc_final: 0.7877 (mtpp) REVERT: A 9 ASP cc_start: 0.7813 (m-30) cc_final: 0.7256 (m-30) REVERT: A 198 MET cc_start: 0.7863 (mtm) cc_final: 0.7524 (ttp) REVERT: B 6 GLN cc_start: 0.7619 (pp30) cc_final: 0.7182 (pp30) REVERT: B 29 THR cc_start: 0.8331 (m) cc_final: 0.7913 (p) REVERT: B 197 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7814 (tpp80) REVERT: G 18 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7838 (tp40) REVERT: S 13 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8131 (tp40) REVERT: S 19 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8298 (tttp) REVERT: S 76 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8269 (mtmm) REVERT: S 89 GLU cc_start: 0.7724 (mp0) cc_final: 0.7496 (mp0) REVERT: S 174 GLN cc_start: 0.8494 (pt0) cc_final: 0.8144 (pt0) REVERT: S 210 GLU cc_start: 0.7849 (mp0) cc_final: 0.7489 (mp0) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2665 time to fit residues: 66.9453 Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 202 ASN R 380 GLN R 396 ASN A 22 ASN A 195 HIS A 213 HIS A 306 GLN B 16 ASN B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN S 167 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9420 Z= 0.177 Angle : 0.544 8.012 12777 Z= 0.276 Chirality : 0.041 0.162 1433 Planarity : 0.003 0.051 1609 Dihedral : 6.222 85.600 1399 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.02 % Allowed : 10.90 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.07 (0.24), residues: 1152 helix: 1.32 (0.27), residues: 395 sheet: -1.96 (0.28), residues: 267 loop : -1.63 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR A 296 ARG 0.005 0.000 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8780 (mt0) cc_final: 0.8416 (mp10) REVERT: R 344 LYS cc_start: 0.8225 (tttt) cc_final: 0.7732 (ttpp) REVERT: A 9 ASP cc_start: 0.7772 (m-30) cc_final: 0.7111 (m-30) REVERT: A 198 MET cc_start: 0.7912 (mtm) cc_final: 0.7693 (ttp) REVERT: A 306 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7820 (mm110) REVERT: B 8 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7779 (mtp85) REVERT: B 29 THR cc_start: 0.8245 (m) cc_final: 0.7764 (p) REVERT: B 66 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (t0) REVERT: B 197 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7979 (tpp80) REVERT: B 254 ASP cc_start: 0.7415 (t70) cc_final: 0.7211 (t70) REVERT: G 18 GLN cc_start: 0.8148 (tp-100) cc_final: 0.7943 (tp40) REVERT: S 13 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8155 (tp40) REVERT: S 19 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8115 (tttp) REVERT: S 76 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8335 (mtmm) REVERT: S 174 GLN cc_start: 0.8559 (pt0) cc_final: 0.8230 (pt0) REVERT: S 210 GLU cc_start: 0.7875 (mp0) cc_final: 0.7537 (mp0) REVERT: S 222 GLU cc_start: 0.7606 (pt0) cc_final: 0.7350 (mp0) REVERT: S 223 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (t80) outliers start: 20 outliers final: 10 residues processed: 168 average time/residue: 0.2565 time to fit residues: 57.0099 Evaluate side-chains 159 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 347 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS S 82 GLN S 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9420 Z= 0.268 Angle : 0.559 9.319 12777 Z= 0.282 Chirality : 0.041 0.152 1433 Planarity : 0.003 0.055 1609 Dihedral : 6.241 87.883 1399 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.72 % Allowed : 13.52 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.74 (0.25), residues: 1152 helix: 1.63 (0.27), residues: 397 sheet: -1.74 (0.27), residues: 279 loop : -1.48 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR A 296 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8727 (mt0) cc_final: 0.8384 (mp10) REVERT: R 230 MET cc_start: 0.7884 (tpp) cc_final: 0.7200 (tpp) REVERT: R 344 LYS cc_start: 0.8322 (tttt) cc_final: 0.7844 (ttpp) REVERT: A 306 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7875 (mm110) REVERT: B 8 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7852 (mtp85) REVERT: B 29 THR cc_start: 0.8270 (m) cc_final: 0.7763 (p) REVERT: B 197 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7961 (tpp80) REVERT: B 254 ASP cc_start: 0.7381 (t70) cc_final: 0.7108 (t0) REVERT: G 22 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8228 (tt0) REVERT: S 13 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8102 (tp40) REVERT: S 19 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8158 (tttp) REVERT: S 73 ASP cc_start: 0.7638 (t70) cc_final: 0.7330 (t70) REVERT: S 76 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8517 (mtmm) REVERT: S 174 GLN cc_start: 0.8574 (pt0) cc_final: 0.8234 (pt0) REVERT: S 210 GLU cc_start: 0.7927 (mp0) cc_final: 0.7656 (mp0) REVERT: S 222 GLU cc_start: 0.7638 (pt0) cc_final: 0.7262 (mp0) REVERT: S 223 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7882 (t80) outliers start: 27 outliers final: 20 residues processed: 166 average time/residue: 0.2510 time to fit residues: 55.6659 Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 29 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9420 Z= 0.153 Angle : 0.496 8.573 12777 Z= 0.251 Chirality : 0.039 0.132 1433 Planarity : 0.003 0.057 1609 Dihedral : 6.046 84.249 1399 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.22 % Allowed : 14.53 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -0.39 (0.25), residues: 1152 helix: 1.87 (0.27), residues: 397 sheet: -1.25 (0.29), residues: 266 loop : -1.47 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 311 PHE 0.010 0.001 PHE A 189 TYR 0.016 0.001 TYR A 302 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8767 (mt0) cc_final: 0.8461 (mp10) REVERT: R 344 LYS cc_start: 0.8265 (tttt) cc_final: 0.7758 (ttpp) REVERT: R 444 LYS cc_start: 0.7162 (tppt) cc_final: 0.6851 (tppt) REVERT: A 302 TYR cc_start: 0.8646 (t80) cc_final: 0.8308 (t80) REVERT: A 306 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7775 (mm110) REVERT: B 8 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7853 (mtt-85) REVERT: B 58 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (pt) REVERT: B 197 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7960 (tpp80) REVERT: B 198 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8467 (pp) REVERT: B 254 ASP cc_start: 0.7481 (t70) cc_final: 0.7123 (t70) REVERT: B 260 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: S 13 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8125 (tp40) REVERT: S 174 GLN cc_start: 0.8551 (pt0) cc_final: 0.8205 (pt0) REVERT: S 210 GLU cc_start: 0.8018 (mp0) cc_final: 0.7677 (mp0) REVERT: S 222 GLU cc_start: 0.7489 (pt0) cc_final: 0.7108 (mp0) REVERT: S 223 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7858 (t80) outliers start: 22 outliers final: 13 residues processed: 164 average time/residue: 0.2413 time to fit residues: 53.1240 Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9420 Z= 0.174 Angle : 0.505 11.979 12777 Z= 0.253 Chirality : 0.039 0.136 1433 Planarity : 0.003 0.060 1609 Dihedral : 6.095 84.516 1399 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.52 % Allowed : 15.64 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: 1152 helix: 1.98 (0.27), residues: 396 sheet: -1.23 (0.29), residues: 271 loop : -1.27 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.017 0.001 TYR A 296 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8768 (mt0) cc_final: 0.8440 (mp10) REVERT: R 344 LYS cc_start: 0.8273 (tttt) cc_final: 0.7773 (ttpp) REVERT: R 444 LYS cc_start: 0.7278 (tppt) cc_final: 0.6929 (tppt) REVERT: A 187 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (p) REVERT: A 306 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7863 (mm110) REVERT: B 8 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7838 (mtt-85) REVERT: B 58 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8200 (pt) REVERT: B 197 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.7945 (tpp80) REVERT: B 198 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8450 (pp) REVERT: B 254 ASP cc_start: 0.7429 (t70) cc_final: 0.7050 (t70) REVERT: B 260 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: G 22 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8368 (tt0) REVERT: G 47 GLU cc_start: 0.8256 (mp0) cc_final: 0.8005 (mt-10) REVERT: S 13 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8146 (tp40) REVERT: S 76 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8452 (mtmm) REVERT: S 174 GLN cc_start: 0.8587 (pt0) cc_final: 0.8275 (pt0) REVERT: S 210 GLU cc_start: 0.7979 (mp0) cc_final: 0.7708 (mp0) REVERT: S 222 GLU cc_start: 0.7565 (pt0) cc_final: 0.7154 (mp0) outliers start: 25 outliers final: 17 residues processed: 164 average time/residue: 0.2328 time to fit residues: 51.7506 Evaluate side-chains 164 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 304 GLN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9420 Z= 0.318 Angle : 0.561 9.968 12777 Z= 0.283 Chirality : 0.041 0.155 1433 Planarity : 0.003 0.060 1609 Dihedral : 6.218 82.968 1399 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.43 % Allowed : 15.54 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -0.28 (0.25), residues: 1152 helix: 1.88 (0.27), residues: 403 sheet: -1.39 (0.28), residues: 286 loop : -1.20 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE B 235 TYR 0.013 0.002 TYR A 296 ARG 0.004 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8754 (mt0) cc_final: 0.8384 (mp10) REVERT: R 344 LYS cc_start: 0.8345 (tttt) cc_final: 0.7889 (ttpp) REVERT: B 8 ARG cc_start: 0.8263 (ttm170) cc_final: 0.8021 (mtp85) REVERT: B 58 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8283 (pt) REVERT: B 197 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.7932 (tpp80) REVERT: B 234 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8866 (m-80) REVERT: B 254 ASP cc_start: 0.7447 (t70) cc_final: 0.7178 (t70) REVERT: B 260 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: G 47 GLU cc_start: 0.8261 (mp0) cc_final: 0.7989 (mt-10) REVERT: S 13 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8284 (tp40) REVERT: S 174 GLN cc_start: 0.8605 (pt0) cc_final: 0.8295 (pt0) REVERT: S 210 GLU cc_start: 0.7969 (mp0) cc_final: 0.7698 (mp0) REVERT: S 222 GLU cc_start: 0.7783 (pt0) cc_final: 0.7474 (mp0) outliers start: 34 outliers final: 24 residues processed: 163 average time/residue: 0.2411 time to fit residues: 53.0354 Evaluate side-chains 165 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9420 Z= 0.220 Angle : 0.526 9.287 12777 Z= 0.265 Chirality : 0.040 0.139 1433 Planarity : 0.003 0.057 1609 Dihedral : 6.149 83.471 1399 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.33 % Allowed : 15.64 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -0.13 (0.25), residues: 1152 helix: 1.96 (0.27), residues: 400 sheet: -1.19 (0.29), residues: 278 loop : -1.14 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.018 0.001 TYR A 296 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8764 (mt0) cc_final: 0.8418 (mp10) REVERT: R 344 LYS cc_start: 0.8315 (tttt) cc_final: 0.7860 (ttpp) REVERT: A 187 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7926 (p) REVERT: A 306 GLN cc_start: 0.7960 (mm110) cc_final: 0.7702 (mm110) REVERT: B 8 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7965 (mtt-85) REVERT: B 58 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8258 (pt) REVERT: B 66 ASP cc_start: 0.8036 (t0) cc_final: 0.7816 (t0) REVERT: B 172 GLU cc_start: 0.8049 (pm20) cc_final: 0.7808 (pm20) REVERT: B 197 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.7993 (tpp80) REVERT: B 234 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8920 (m-80) REVERT: B 254 ASP cc_start: 0.7414 (t70) cc_final: 0.7129 (t70) REVERT: B 260 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: G 47 GLU cc_start: 0.8259 (mp0) cc_final: 0.8003 (mt-10) REVERT: S 13 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8248 (tp40) REVERT: S 76 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8059 (mtmm) REVERT: S 174 GLN cc_start: 0.8608 (pt0) cc_final: 0.8303 (pt0) REVERT: S 210 GLU cc_start: 0.7979 (mp0) cc_final: 0.7641 (mp0) REVERT: S 222 GLU cc_start: 0.7720 (pt0) cc_final: 0.7484 (mp0) outliers start: 33 outliers final: 24 residues processed: 168 average time/residue: 0.2217 time to fit residues: 51.0385 Evaluate side-chains 170 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 304 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9420 Z= 0.224 Angle : 0.534 9.306 12777 Z= 0.269 Chirality : 0.040 0.141 1433 Planarity : 0.003 0.060 1609 Dihedral : 6.110 81.211 1399 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.04 % Allowed : 15.84 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -0.09 (0.25), residues: 1152 helix: 1.96 (0.27), residues: 400 sheet: -1.10 (0.29), residues: 278 loop : -1.14 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR A 302 ARG 0.003 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8760 (mt0) cc_final: 0.8407 (mp10) REVERT: R 344 LYS cc_start: 0.8315 (tttt) cc_final: 0.7864 (ttpp) REVERT: R 537 TRP cc_start: 0.7738 (m-10) cc_final: 0.7482 (m-10) REVERT: A 198 MET cc_start: 0.7982 (ttm) cc_final: 0.7782 (ttm) REVERT: A 306 GLN cc_start: 0.7982 (mm110) cc_final: 0.7722 (mm110) REVERT: B 58 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8255 (pt) REVERT: B 66 ASP cc_start: 0.8039 (t0) cc_final: 0.7814 (t0) REVERT: B 197 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8010 (tpp80) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8914 (m-80) REVERT: B 254 ASP cc_start: 0.7414 (t70) cc_final: 0.7136 (t70) REVERT: B 260 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: G 22 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8259 (tt0) REVERT: G 47 GLU cc_start: 0.8210 (mp0) cc_final: 0.7975 (mt-10) REVERT: S 13 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8176 (tp40) REVERT: S 76 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8033 (mtmm) REVERT: S 174 GLN cc_start: 0.8603 (pt0) cc_final: 0.8297 (pt0) REVERT: S 210 GLU cc_start: 0.7994 (mp0) cc_final: 0.7726 (mp0) REVERT: S 222 GLU cc_start: 0.7678 (pt0) cc_final: 0.7385 (mm-30) outliers start: 40 outliers final: 30 residues processed: 166 average time/residue: 0.2262 time to fit residues: 51.3525 Evaluate side-chains 174 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 255 ASP Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9420 Z= 0.181 Angle : 0.523 9.575 12777 Z= 0.261 Chirality : 0.040 0.133 1433 Planarity : 0.003 0.058 1609 Dihedral : 6.032 81.847 1399 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.83 % Allowed : 17.05 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -0.00 (0.25), residues: 1152 helix: 2.07 (0.27), residues: 398 sheet: -1.06 (0.29), residues: 280 loop : -1.10 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE A 189 TYR 0.015 0.001 TYR A 302 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8783 (mt0) cc_final: 0.8437 (mp10) REVERT: R 344 LYS cc_start: 0.8270 (tttt) cc_final: 0.7794 (ttpp) REVERT: R 537 TRP cc_start: 0.7733 (m-10) cc_final: 0.7511 (m-10) REVERT: A 187 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 298 GLU cc_start: 0.8666 (mp0) cc_final: 0.8118 (mp0) REVERT: A 306 GLN cc_start: 0.7985 (mm110) cc_final: 0.7715 (mm110) REVERT: B 8 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7893 (mtp85) REVERT: B 58 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8170 (pt) REVERT: B 130 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8337 (mp0) REVERT: B 197 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7940 (tpp80) REVERT: B 214 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8181 (mtt-85) REVERT: B 234 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8952 (m-80) REVERT: B 254 ASP cc_start: 0.7398 (t70) cc_final: 0.7121 (t70) REVERT: B 260 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 325 MET cc_start: 0.8594 (tpp) cc_final: 0.8350 (tpp) REVERT: G 22 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8275 (tt0) REVERT: G 47 GLU cc_start: 0.8142 (mp0) cc_final: 0.7930 (mt-10) REVERT: S 13 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8201 (tp40) REVERT: S 76 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8047 (mtmm) REVERT: S 174 GLN cc_start: 0.8584 (pt0) cc_final: 0.8286 (pt0) REVERT: S 210 GLU cc_start: 0.8033 (mp0) cc_final: 0.7762 (mp0) REVERT: S 222 GLU cc_start: 0.7660 (pt0) cc_final: 0.7380 (mm-30) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.2355 time to fit residues: 53.2082 Evaluate side-chains 171 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 433 HIS A 22 ASN A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.003 0.048 9420 Z= 0.186 Angle : 0.531 9.716 12777 Z= 0.264 Chirality : 0.040 0.133 1433 Planarity : 0.003 0.061 1609 Dihedral : 5.989 80.470 1399 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.83 % Allowed : 17.36 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: 0.06 (0.25), residues: 1152 helix: 2.11 (0.27), residues: 398 sheet: -0.99 (0.30), residues: 280 loop : -1.08 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE A 189 TYR 0.022 0.001 TYR A 296 ARG 0.002 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8754 (mt0) cc_final: 0.8416 (mp10) REVERT: R 344 LYS cc_start: 0.8269 (tttt) cc_final: 0.7796 (ttpp) REVERT: A 187 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7929 (p) REVERT: A 298 GLU cc_start: 0.8653 (mp0) cc_final: 0.8106 (mp0) REVERT: A 306 GLN cc_start: 0.8000 (mm110) cc_final: 0.7733 (mm110) REVERT: B 8 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7899 (mtp85) REVERT: B 58 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 130 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8333 (mp0) REVERT: B 197 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.7941 (tpp80) REVERT: B 214 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8196 (mtt-85) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 254 ASP cc_start: 0.7371 (t70) cc_final: 0.7113 (t70) REVERT: B 260 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: G 22 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8286 (tt0) REVERT: G 47 GLU cc_start: 0.8162 (mp0) cc_final: 0.7898 (mt-10) REVERT: S 13 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8221 (tp40) REVERT: S 76 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8048 (mtmm) REVERT: S 174 GLN cc_start: 0.8595 (pt0) cc_final: 0.8296 (pt0) REVERT: S 210 GLU cc_start: 0.8010 (mp0) cc_final: 0.7737 (mp0) outliers start: 28 outliers final: 22 residues processed: 164 average time/residue: 0.2249 time to fit residues: 50.4546 Evaluate side-chains 169 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 0.0170 chunk 80 optimal weight: 0.3980 chunk 5 optimal weight: 9.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 311 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.131998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100321 restraints weight = 13508.271| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.99 r_work: 0.3077 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9420 Z= 0.132 Angle : 0.520 9.927 12777 Z= 0.258 Chirality : 0.039 0.141 1433 Planarity : 0.003 0.056 1609 Dihedral : 5.877 81.840 1399 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 18.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.20 (0.25), residues: 1152 helix: 2.21 (0.27), residues: 397 sheet: -0.77 (0.31), residues: 271 loop : -1.07 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.000 HIS B 311 PHE 0.008 0.001 PHE A 189 TYR 0.030 0.001 TYR A 296 ARG 0.001 0.000 ARG R 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.86 seconds wall clock time: 41 minutes 33.42 seconds (2493.42 seconds total)