Starting phenix.real_space_refine on Sun Mar 17 10:53:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irs_35684/03_2024/8irs_35684_neut_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5603 2.51 5 N 1479 2.21 5 O 1646 1.98 5 H 8717 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 208": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 145": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 17510 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3607 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5118 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3516 Classifications: {'peptide': 233} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 900 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4369 Unusual residues: {'R5F': 1} Classifications: {'peptide': 264, 'undetermined': 1} Link IDs: {'PTRANS': 9, 'TRANS': 254, None: 1} Not linked: pdbres="LEU R 441 " pdbres="R5F R 501 " Chain breaks: 1 Time building chain proxies: 7.90, per 1000 atoms: 0.45 Number of scatterers: 17510 At special positions: 0 Unit cell: (99.275, 125.4, 119.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 O 1646 8.00 N 1479 7.00 C 5603 6.00 H 8717 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " 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: 14.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 12 sheets defined 36.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 removed outlier: 3.518A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 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 217 removed outlier: 3.623A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.416A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.070A 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 310 removed outlier: 3.837A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 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 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 35 through 61 removed outlier: 3.539A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 65 No H-bonds generated for 'chain 'R' and resid 63 through 65' Processing helix chain 'R' and resid 68 through 86 removed outlier: 3.517A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 97 Processing helix chain 'R' and resid 104 through 137 removed outlier: 3.558A pdb=" N VAL R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 145 through 171 removed outlier: 3.638A pdb=" N LYS R 149 " --> pdb=" O ARG R 145 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 187 through 197 Processing helix chain 'R' and resid 199 through 213 Processing helix chain 'R' and resid 368 through 398 removed outlier: 3.571A pdb=" N VAL R 378 " --> pdb=" O LEU R 375 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU R 379 " --> pdb=" O ALA R 376 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE R 383 " --> pdb=" O GLY R 380 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N CYS R 385 " --> pdb=" O PHE R 382 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TRP R 386 " --> pdb=" O ILE R 383 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU R 387 " --> pdb=" O ILE R 384 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 3.627A pdb=" N ILE R 391 " --> pdb=" O PRO R 388 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS R 393 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASN R 396 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 428 removed outlier: 3.655A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 431 through 440 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.021A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.031A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.623A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.624A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.607A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.546A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.677A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.707A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.809A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.395A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1071 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: 6.75 Time building geometry restraints manager: 15.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 1979 1.02 - 1.22: 6746 1.22 - 1.42: 3839 1.42 - 1.62: 5030 1.62 - 1.82: 95 Bond restraints: 17689 Sorted by residual: bond pdb=" C7 R5F R 501 " pdb=" C8 R5F R 501 " ideal model delta sigma weight residual 1.596 1.383 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.743 -0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C9 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.717 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CD2 PHE A 250 " pdb=" HD2 PHE A 250 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ASP G 26 " pdb=" H ASP G 26 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 17684 not shown) Histogram of bond angle deviations from ideal: 88.75 - 97.95: 27 97.95 - 107.16: 1733 107.16 - 116.36: 19795 116.36 - 125.57: 9954 125.57 - 134.78: 350 Bond angle restraints: 31859 Sorted by residual: angle pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " ideal model delta sigma weight residual 116.34 123.70 -7.36 1.04e+00 9.25e-01 5.01e+01 angle pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " pdb=" C9 R5F R 501 " ideal model delta sigma weight residual 107.56 88.75 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C ARG E 191 " pdb=" CA ARG E 191 " pdb=" CB ARG E 191 " ideal model delta sigma weight residual 113.37 123.31 -9.94 1.61e+00 3.86e-01 3.81e+01 angle pdb=" CA ASN E 171 " pdb=" CB ASN E 171 " pdb=" CG ASN E 171 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 109.07 117.45 -8.38 1.52e+00 4.33e-01 3.04e+01 ... (remaining 31854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 7575 17.46 - 34.92: 516 34.92 - 52.38: 114 52.38 - 69.83: 136 69.83 - 87.29: 10 Dihedral angle restraints: 8351 sinusoidal: 4475 harmonic: 3876 Sorted by residual: dihedral pdb=" CA ILE R 214 " pdb=" C ILE R 214 " pdb=" N VAL R 215 " pdb=" CA VAL R 215 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU B 284 " pdb=" C LEU B 284 " pdb=" N LEU B 285 " pdb=" CA LEU B 285 " ideal model delta harmonic sigma weight residual 180.00 150.97 29.03 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 8348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 957 0.095 - 0.191: 363 0.191 - 0.286: 54 0.286 - 0.382: 12 0.382 - 0.477: 7 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA GLU A 238 " pdb=" N GLU A 238 " pdb=" C GLU A 238 " pdb=" CB GLU A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA ASP B 186 " pdb=" N ASP B 186 " pdb=" C ASP B 186 " pdb=" CB ASP B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 1390 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 175 " -0.292 2.00e-02 2.50e+03 1.25e-01 4.71e+02 pdb=" CG TYR E 175 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR E 175 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR E 175 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 TYR E 175 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TYR E 175 " 0.074 2.00e-02 2.50e+03 pdb=" CZ TYR E 175 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR E 175 " -0.248 2.00e-02 2.50e+03 pdb=" HD1 TYR E 175 " 0.081 2.00e-02 2.50e+03 pdb=" HD2 TYR E 175 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR E 175 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR E 175 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 413 " 0.242 2.00e-02 2.50e+03 8.72e-02 3.04e+02 pdb=" CG TRP R 413 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP R 413 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP R 413 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP R 413 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP R 413 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP R 413 " -0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 413 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 413 " -0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP R 413 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 TRP R 413 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP R 413 " -0.092 2.00e-02 2.50e+03 pdb=" HE3 TRP R 413 " -0.120 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 413 " 0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 413 " -0.050 2.00e-02 2.50e+03 pdb=" HH2 TRP R 413 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 22 " 0.003 9.50e-02 1.11e+02 1.14e-01 2.90e+02 pdb=" NE ARG B 22 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 22 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG B 22 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG B 22 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG B 22 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 22 " 0.165 2.00e-02 2.50e+03 pdb="HH21 ARG B 22 " 0.200 2.00e-02 2.50e+03 pdb="HH22 ARG B 22 " -0.205 2.00e-02 2.50e+03 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1404 2.20 - 2.80: 33352 2.80 - 3.40: 51152 3.40 - 4.00: 68528 4.00 - 4.60: 100179 Nonbonded interactions: 254615 Sorted by model distance: nonbonded pdb=" OD1 ASP R 80 " pdb=" HG SER R 419 " model vdw 1.600 1.850 nonbonded pdb=" OD2 ASP B 170 " pdb=" HG1 THR B 173 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.610 1.850 nonbonded pdb=" OD1 ASP B 163 " pdb=" HG1 THR B 165 " model vdw 1.613 1.850 nonbonded pdb=" HH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 1.620 1.850 ... (remaining 254610 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: 0.400 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: 0.240 Extract box with map and model: 2.410 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 57.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.013 0.213 8972 Z= 0.832 Angle : 1.864 18.815 12158 Z= 1.233 Chirality : 0.100 0.477 1393 Planarity : 0.017 0.198 1529 Dihedral : 12.737 87.292 3227 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 3.33 % 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: -1.14 (0.24), residues: 1102 helix: -0.92 (0.22), residues: 395 sheet: -0.34 (0.31), residues: 262 loop : -0.63 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.164 0.026 TRP B 99 HIS 0.014 0.004 HIS B 54 PHE 0.090 0.016 PHE A 259 TYR 0.251 0.027 TYR E 175 ARG 0.010 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7573 (tt0) cc_final: 0.7355 (tt0) REVERT: A 32 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7840 (mtp85) REVERT: A 251 ASP cc_start: 0.7884 (t0) cc_final: 0.7554 (t0) REVERT: A 252 SER cc_start: 0.8126 (t) cc_final: 0.7908 (t) REVERT: B 46 ARG cc_start: 0.7556 (mtp-110) cc_final: 0.7211 (ttm-80) REVERT: B 181 THR cc_start: 0.7631 (p) cc_final: 0.7375 (m) REVERT: B 188 MET cc_start: 0.8204 (mmm) cc_final: 0.7957 (mmm) REVERT: R 50 PHE cc_start: 0.8239 (t80) cc_final: 0.8002 (t80) REVERT: R 63 LYS cc_start: 0.7756 (tttt) cc_final: 0.7539 (tttp) REVERT: R 164 PHE cc_start: 0.8294 (t80) cc_final: 0.8089 (t80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 2.1672 time to fit residues: 741.7087 Evaluate side-chains 223 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 346 ASN B 6 GLN B 13 GLN B 259 GLN G 24 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8972 Z= 0.217 Angle : 0.632 7.871 12158 Z= 0.341 Chirality : 0.042 0.162 1393 Planarity : 0.004 0.048 1529 Dihedral : 7.097 59.825 1221 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.24 % Allowed : 13.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.14 (0.25), residues: 1102 helix: 0.65 (0.25), residues: 403 sheet: -0.43 (0.30), residues: 271 loop : -0.39 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE R 189 TYR 0.035 0.002 TYR B 105 ARG 0.007 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8124 (mtm180) cc_final: 0.7811 (mtp85) REVERT: A 53 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7169 (mtp) REVERT: B 46 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7154 (mtp85) REVERT: B 181 THR cc_start: 0.7729 (p) cc_final: 0.7507 (m) REVERT: B 280 LYS cc_start: 0.8039 (tttm) cc_final: 0.7827 (ttmm) REVERT: E 140 MET cc_start: 0.8613 (mmm) cc_final: 0.7968 (mmt) REVERT: R 63 LYS cc_start: 0.7946 (tttt) cc_final: 0.7690 (tttp) REVERT: R 78 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7613 (t) REVERT: R 134 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8029 (t) outliers start: 41 outliers final: 13 residues processed: 267 average time/residue: 2.2254 time to fit residues: 639.2310 Evaluate side-chains 226 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 237 ASN B 239 ASN B 259 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8972 Z= 0.209 Angle : 0.565 6.367 12158 Z= 0.305 Chirality : 0.041 0.153 1393 Planarity : 0.004 0.056 1529 Dihedral : 6.296 54.987 1221 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.62 % Allowed : 17.39 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.25 (0.25), residues: 1102 helix: 1.22 (0.26), residues: 402 sheet: -0.45 (0.29), residues: 268 loop : -0.28 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.002 PHE R 189 TYR 0.021 0.001 TYR B 105 ARG 0.008 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7825 (mtp85) REVERT: B 46 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7284 (ttm-80) REVERT: B 217 MET cc_start: 0.7831 (ptm) cc_final: 0.7614 (ppp) REVERT: B 280 LYS cc_start: 0.8018 (tttm) cc_final: 0.7776 (ttmm) REVERT: G 21 MET cc_start: 0.8183 (ttm) cc_final: 0.7958 (ttm) REVERT: R 134 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8154 (t) REVERT: R 149 LYS cc_start: 0.8415 (tppp) cc_final: 0.8145 (tppp) REVERT: R 440 ILE cc_start: 0.8154 (mm) cc_final: 0.7928 (tp) outliers start: 35 outliers final: 12 residues processed: 238 average time/residue: 2.2041 time to fit residues: 564.3873 Evaluate side-chains 214 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 393 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN B 259 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8972 Z= 0.335 Angle : 0.587 6.856 12158 Z= 0.318 Chirality : 0.042 0.151 1393 Planarity : 0.004 0.059 1529 Dihedral : 6.121 52.991 1221 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.62 % Allowed : 19.67 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.25), residues: 1102 helix: 1.37 (0.26), residues: 395 sheet: -0.65 (0.29), residues: 281 loop : -0.55 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 99 HIS 0.006 0.001 HIS B 183 PHE 0.017 0.002 PHE B 235 TYR 0.020 0.002 TYR B 105 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8321 (mtm180) cc_final: 0.7978 (mtp85) REVERT: B 46 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7257 (mtp85) REVERT: B 214 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7650 (mmp80) REVERT: B 217 MET cc_start: 0.7993 (ptm) cc_final: 0.7711 (ppp) REVERT: B 275 SER cc_start: 0.8948 (t) cc_final: 0.8582 (m) REVERT: B 280 LYS cc_start: 0.7992 (tttm) cc_final: 0.7771 (ttmm) REVERT: B 303 ASP cc_start: 0.7784 (m-30) cc_final: 0.7393 (p0) REVERT: E 186 GLN cc_start: 0.7524 (mt0) cc_final: 0.7302 (mm110) REVERT: R 116 MET cc_start: 0.7507 (ttt) cc_final: 0.7129 (tpp) REVERT: R 134 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8217 (t) REVERT: R 440 ILE cc_start: 0.8199 (mm) cc_final: 0.7978 (tp) outliers start: 35 outliers final: 22 residues processed: 237 average time/residue: 2.1097 time to fit residues: 541.4326 Evaluate side-chains 224 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 154 VAL Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 0.0870 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN B 259 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8972 Z= 0.219 Angle : 0.540 6.157 12158 Z= 0.288 Chirality : 0.041 0.143 1393 Planarity : 0.003 0.062 1529 Dihedral : 5.851 53.470 1221 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.21 % Allowed : 21.95 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.27 (0.25), residues: 1102 helix: 1.56 (0.26), residues: 396 sheet: -0.63 (0.29), residues: 281 loop : -0.44 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.013 0.002 PHE R 390 TYR 0.016 0.001 TYR E 190 ARG 0.010 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7979 (mtp85) REVERT: A 197 LYS cc_start: 0.8106 (mttp) cc_final: 0.7867 (mtpt) REVERT: B 46 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7237 (mtp85) REVERT: B 217 MET cc_start: 0.8012 (ptm) cc_final: 0.7750 (ppp) REVERT: B 275 SER cc_start: 0.8876 (t) cc_final: 0.8516 (m) REVERT: E 186 GLN cc_start: 0.7470 (mt0) cc_final: 0.7236 (mm-40) REVERT: R 116 MET cc_start: 0.7462 (ttt) cc_final: 0.7117 (tpp) REVERT: R 134 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (t) REVERT: R 149 LYS cc_start: 0.8366 (tppp) cc_final: 0.8020 (tppp) REVERT: R 440 ILE cc_start: 0.8140 (mm) cc_final: 0.7924 (tp) outliers start: 31 outliers final: 19 residues processed: 225 average time/residue: 2.0923 time to fit residues: 509.3131 Evaluate side-chains 216 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 13 GLN B 259 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 66 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8972 Z= 0.221 Angle : 0.530 5.453 12158 Z= 0.283 Chirality : 0.040 0.139 1393 Planarity : 0.003 0.057 1529 Dihedral : 5.685 54.641 1221 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.42 % Allowed : 22.67 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1102 helix: 1.74 (0.26), residues: 393 sheet: -0.70 (0.29), residues: 283 loop : -0.42 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.001 PHE R 390 TYR 0.015 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7983 (mtp85) REVERT: B 46 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7251 (mtp85) REVERT: B 217 MET cc_start: 0.8028 (ptm) cc_final: 0.7756 (ppp) REVERT: B 275 SER cc_start: 0.8836 (t) cc_final: 0.8507 (m) REVERT: B 318 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7605 (mp) REVERT: R 134 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8259 (t) REVERT: R 149 LYS cc_start: 0.8397 (tppp) cc_final: 0.8096 (tppp) outliers start: 33 outliers final: 22 residues processed: 227 average time/residue: 2.0600 time to fit residues: 505.7166 Evaluate side-chains 219 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN R 66 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8972 Z= 0.181 Angle : 0.515 4.899 12158 Z= 0.273 Chirality : 0.040 0.140 1393 Planarity : 0.003 0.066 1529 Dihedral : 5.554 56.478 1221 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.31 % Allowed : 23.40 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.44 (0.26), residues: 1102 helix: 1.85 (0.26), residues: 395 sheet: -0.70 (0.29), residues: 287 loop : -0.36 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.001 PHE R 390 TYR 0.013 0.001 TYR E 190 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7813 (p0) cc_final: 0.7577 (m110) REVERT: A 32 ARG cc_start: 0.8285 (mtm180) cc_final: 0.8020 (mtp85) REVERT: B 46 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7254 (mtp85) REVERT: B 214 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7665 (mmp80) REVERT: B 217 MET cc_start: 0.7977 (ptm) cc_final: 0.7682 (ppp) REVERT: B 275 SER cc_start: 0.8856 (t) cc_final: 0.8519 (m) REVERT: B 318 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7546 (mp) REVERT: G 41 CYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8200 (m) REVERT: R 134 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8235 (t) REVERT: R 149 LYS cc_start: 0.8326 (tppp) cc_final: 0.8048 (tppp) outliers start: 32 outliers final: 18 residues processed: 228 average time/residue: 2.0633 time to fit residues: 508.8805 Evaluate side-chains 223 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 62 HIS ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8972 Z= 0.313 Angle : 0.566 6.001 12158 Z= 0.302 Chirality : 0.041 0.141 1393 Planarity : 0.004 0.075 1529 Dihedral : 5.639 57.197 1221 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.42 % Allowed : 23.71 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.26 (0.25), residues: 1102 helix: 1.81 (0.27), residues: 387 sheet: -0.79 (0.29), residues: 278 loop : -0.56 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 36 HIS 0.006 0.001 HIS B 183 PHE 0.014 0.002 PHE B 235 TYR 0.017 0.002 TYR E 190 ARG 0.011 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 208 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8308 (mtm180) cc_final: 0.8029 (mtp85) REVERT: B 46 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7344 (mtp85) REVERT: B 214 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7652 (mmp80) REVERT: B 217 MET cc_start: 0.8046 (ptm) cc_final: 0.7734 (ppp) REVERT: B 275 SER cc_start: 0.8877 (t) cc_final: 0.8518 (m) REVERT: B 318 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 116 MET cc_start: 0.7610 (ttt) cc_final: 0.6929 (tpp) REVERT: R 134 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8281 (t) REVERT: R 149 LYS cc_start: 0.8388 (tppp) cc_final: 0.8109 (tppp) outliers start: 33 outliers final: 25 residues processed: 232 average time/residue: 1.9946 time to fit residues: 503.6432 Evaluate side-chains 229 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8972 Z= 0.195 Angle : 0.542 5.204 12158 Z= 0.285 Chirality : 0.040 0.143 1393 Planarity : 0.004 0.081 1529 Dihedral : 5.528 58.019 1221 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.00 % Allowed : 24.53 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1102 helix: 1.95 (0.27), residues: 386 sheet: -0.77 (0.29), residues: 289 loop : -0.54 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 160 HIS 0.006 0.001 HIS B 183 PHE 0.013 0.001 PHE R 390 TYR 0.013 0.001 TYR A 302 ARG 0.014 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7920 (p0) cc_final: 0.7686 (m-40) REVERT: A 32 ARG cc_start: 0.8303 (mtm180) cc_final: 0.8015 (mtp85) REVERT: B 46 ARG cc_start: 0.7626 (mtp-110) cc_final: 0.7388 (ttm-80) REVERT: B 214 ARG cc_start: 0.7924 (mmp80) cc_final: 0.7648 (mmp80) REVERT: B 217 MET cc_start: 0.8025 (ptm) cc_final: 0.7736 (ppp) REVERT: B 275 SER cc_start: 0.8846 (t) cc_final: 0.8511 (m) REVERT: B 318 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7574 (mp) REVERT: G 41 CYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8296 (m) REVERT: R 116 MET cc_start: 0.7527 (ttt) cc_final: 0.7098 (tpp) REVERT: R 134 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8248 (t) REVERT: R 149 LYS cc_start: 0.8352 (tppp) cc_final: 0.8094 (tppp) outliers start: 29 outliers final: 21 residues processed: 225 average time/residue: 1.9978 time to fit residues: 487.8564 Evaluate side-chains 219 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8972 Z= 0.186 Angle : 0.531 5.432 12158 Z= 0.279 Chirality : 0.040 0.140 1393 Planarity : 0.004 0.083 1529 Dihedral : 5.473 58.617 1221 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.59 % Allowed : 25.05 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.25), residues: 1102 helix: 2.05 (0.27), residues: 386 sheet: -0.77 (0.29), residues: 294 loop : -0.48 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR E 190 ARG 0.014 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8304 (mtm180) cc_final: 0.8042 (mtp85) REVERT: B 46 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7389 (ttm-80) REVERT: B 214 ARG cc_start: 0.7920 (mmp80) cc_final: 0.7646 (mmp80) REVERT: B 217 MET cc_start: 0.8000 (ptm) cc_final: 0.7705 (ppp) REVERT: B 275 SER cc_start: 0.8855 (t) cc_final: 0.8503 (m) REVERT: B 325 MET cc_start: 0.8302 (tpp) cc_final: 0.7902 (tpt) REVERT: G 41 CYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8292 (m) REVERT: R 57 MET cc_start: 0.8360 (mtt) cc_final: 0.7958 (mmt) REVERT: R 116 MET cc_start: 0.7421 (ttt) cc_final: 0.7013 (tpp) REVERT: R 134 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8198 (t) REVERT: R 149 LYS cc_start: 0.8295 (tppp) cc_final: 0.8045 (tppp) outliers start: 25 outliers final: 19 residues processed: 225 average time/residue: 2.0066 time to fit residues: 490.0224 Evaluate side-chains 225 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 134 THR Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128828 restraints weight = 29037.062| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.42 r_work: 0.3450 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8972 Z= 0.224 Angle : 0.540 5.430 12158 Z= 0.285 Chirality : 0.040 0.142 1393 Planarity : 0.004 0.083 1529 Dihedral : 5.458 58.964 1221 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.80 % Allowed : 25.26 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.39 (0.25), residues: 1102 helix: 1.95 (0.27), residues: 387 sheet: -0.74 (0.29), residues: 283 loop : -0.51 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 413 HIS 0.006 0.001 HIS B 183 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR B 264 ARG 0.014 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8922.68 seconds wall clock time: 156 minutes 7.18 seconds (9367.18 seconds total)