Starting phenix.real_space_refine on Fri Feb 16 20:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xz6_33526/02_2024/7xz6_33526_trim_updated.pdb" } resolution = 2.8 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= 0.007 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: 6 Type Number sf(0) Gaussians S 57 5.16 5 C 5238 2.51 5 N 1437 2.21 5 O 1533 1.98 5 F 1 1.80 5 H 8192 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 265": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 342": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 374": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 380": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 389": "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 PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 226": "OE1" <-> "OE2" 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 "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 225": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 285": "OE1" <-> "OE2" Residue "R ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16458 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3910 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4645 Unusual residues: {'I7J': 1} Classifications: {'peptide': 292, 'undetermined': 1, 'water': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282, None: 2} Not linked: pdbres="VAL R 300 " pdbres="I7J R 401 " Not linked: pdbres="I7J R 401 " pdbres="HOH R 501 " Chain breaks: 1 Time building chain proxies: 8.04, per 1000 atoms: 0.49 Number of scatterers: 16458 At special positions: 0 Unit cell: (100.32, 98.23, 115.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 F 1 9.00 O 1533 8.00 N 1437 7.00 C 5238 6.00 H 8192 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.05 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: 13.69 Conformation dependent library (CDL) restraints added in 1.7 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 39.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.469A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 3.566A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 removed outlier: 4.271A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 2 through 35 Processing helix chain 'R' and resid 40 through 65 removed outlier: 3.524A pdb=" N LEU R 62 " --> pdb=" O ILE R 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 108 removed outlier: 3.710A pdb=" N THR R 76 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS R 78 " --> pdb=" O LYS R 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS R 108 " --> pdb=" O LEU R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 116 removed outlier: 3.623A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 142 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 171 Processing helix chain 'R' and resid 174 through 209 Processing helix chain 'R' and resid 220 through 250 removed outlier: 3.722A pdb=" N ALA R 223 " --> pdb=" O ASP R 220 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR R 239 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 257 through 262 Processing helix chain 'R' and resid 264 through 279 removed outlier: 4.016A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 284 through 298 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.376A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, 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: 4.641A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.443A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.321A 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: 6.732A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.390A 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: 4.949A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.914A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.493A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.669A 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: 6.335A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.876A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 972 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: 5.91 Time building geometry restraints manager: 14.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8169 1.04 - 1.25: 1337 1.25 - 1.46: 2546 1.46 - 1.66: 4487 1.66 - 1.87: 83 Bond restraints: 16622 Sorted by residual: bond pdb=" C18 I7J R 401 " pdb=" S1 I7J R 401 " ideal model delta sigma weight residual 1.781 1.867 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C12 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.353 1.422 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C4 I7J R 401 " pdb=" N1 I7J R 401 " ideal model delta sigma weight residual 1.357 1.425 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 I7J R 401 " pdb=" O3 I7J R 401 " ideal model delta sigma weight residual 1.313 1.372 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" C15 I7J R 401 " pdb=" N5 I7J R 401 " ideal model delta sigma weight residual 1.402 1.458 -0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 16617 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.72: 1205 107.72 - 115.14: 19666 115.14 - 122.56: 6848 122.56 - 129.97: 2136 129.97 - 137.39: 57 Bond angle restraints: 29912 Sorted by residual: angle pdb=" CA CYS R 254 " pdb=" CB CYS R 254 " pdb=" SG CYS R 254 " ideal model delta sigma weight residual 114.40 124.15 -9.75 2.30e+00 1.89e-01 1.80e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 112.29 108.54 3.75 9.40e-01 1.13e+00 1.59e+01 angle pdb=" CA CYS R 251 " pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " ideal model delta sigma weight residual 114.40 122.30 -7.90 2.30e+00 1.89e-01 1.18e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.44 114.13 -3.69 1.20e+00 6.94e-01 9.47e+00 angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 112.96 109.90 3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 29907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7231 17.51 - 35.01: 437 35.01 - 52.52: 121 52.52 - 70.02: 45 70.02 - 87.53: 14 Dihedral angle restraints: 7848 sinusoidal: 4236 harmonic: 3612 Sorted by residual: dihedral pdb=" CB CYS R 251 " pdb=" SG CYS R 251 " pdb=" SG CYS R 254 " pdb=" CB CYS R 254 " ideal model delta sinusoidal sigma weight residual -86.00 0.40 -86.40 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA GLU R 253 " pdb=" C GLU R 253 " pdb=" N CYS R 254 " pdb=" CA CYS R 254 " ideal model delta harmonic sigma weight residual -180.00 -150.20 -29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LEU G 19 " pdb=" C LEU G 19 " pdb=" N LYS G 20 " pdb=" CA LYS G 20 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 880 0.030 - 0.060: 263 0.060 - 0.089: 87 0.089 - 0.119: 50 0.119 - 0.149: 9 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CG LEU G 19 " pdb=" CB LEU G 19 " pdb=" CD1 LEU G 19 " pdb=" CD2 LEU G 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE R 143 " pdb=" N ILE R 143 " pdb=" C ILE R 143 " pdb=" CB ILE R 143 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1286 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 162 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO R 163 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 163 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 163 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO G 60 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 175 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO R 176 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 176 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 176 " 0.015 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 540 2.13 - 2.74: 30591 2.74 - 3.36: 49535 3.36 - 3.98: 63634 3.98 - 4.60: 99235 Nonbonded interactions: 243535 Sorted by model distance: nonbonded pdb="HD21 ASN B 340 " pdb="HD22 ASN G 59 " model vdw 1.507 2.100 nonbonded pdb=" OE1 GLN R 109 " pdb="HH21 ARG R 112 " model vdw 1.534 1.850 nonbonded pdb=" O ALA R 91 " pdb=" HG1 THR R 95 " model vdw 1.538 1.850 nonbonded pdb=" OD1 ASP B 290 " pdb=" HE ARG B 314 " model vdw 1.592 1.850 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.592 1.850 ... (remaining 243530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.160 Extract box with map and model: 3.060 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 56.190 Find NCS groups from input model: 0.280 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 8430 Z= 0.232 Angle : 0.559 9.747 11413 Z= 0.310 Chirality : 0.038 0.149 1289 Planarity : 0.002 0.032 1451 Dihedral : 12.807 87.527 3065 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1036 helix: 2.81 (0.26), residues: 407 sheet: 0.07 (0.36), residues: 216 loop : 0.47 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 281 HIS 0.008 0.001 HIS R 292 PHE 0.013 0.001 PHE B 234 TYR 0.008 0.001 TYR R 185 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7277 (m-30) cc_final: 0.7049 (m-30) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 2.3916 time to fit residues: 493.7690 Evaluate side-chains 149 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN G 18 GLN N 31 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8430 Z= 0.276 Angle : 0.550 8.204 11413 Z= 0.308 Chirality : 0.040 0.150 1289 Planarity : 0.005 0.040 1451 Dihedral : 5.013 28.128 1174 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.02 % Allowed : 9.99 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1036 helix: 1.78 (0.26), residues: 407 sheet: -0.10 (0.35), residues: 210 loop : 0.33 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE G 61 TYR 0.016 0.002 TYR B 59 ARG 0.005 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7522 (mmt180) cc_final: 0.7308 (mmt-90) REVERT: B 186 ASP cc_start: 0.7791 (m-30) cc_final: 0.7573 (m-30) REVERT: G 16 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7023 (t) REVERT: N 5 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: N 120 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7136 (mm-40) outliers start: 18 outliers final: 10 residues processed: 157 average time/residue: 2.4399 time to fit residues: 409.3350 Evaluate side-chains 146 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8430 Z= 0.223 Angle : 0.509 7.560 11413 Z= 0.282 Chirality : 0.039 0.155 1289 Planarity : 0.005 0.036 1451 Dihedral : 4.863 24.589 1172 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 12.91 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1036 helix: 1.31 (0.26), residues: 413 sheet: -0.25 (0.34), residues: 212 loop : 0.33 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 82 HIS 0.006 0.001 HIS A 41 PHE 0.014 0.002 PHE R 161 TYR 0.012 0.001 TYR R 185 ARG 0.002 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7632 (m-30) cc_final: 0.7388 (m-30) REVERT: N 5 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: N 120 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7094 (mm-40) outliers start: 13 outliers final: 8 residues processed: 147 average time/residue: 2.5683 time to fit residues: 402.0747 Evaluate side-chains 139 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 254 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8430 Z= 0.238 Angle : 0.509 7.311 11413 Z= 0.280 Chirality : 0.039 0.139 1289 Planarity : 0.004 0.043 1451 Dihedral : 4.835 24.638 1172 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.24 % Allowed : 13.47 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1036 helix: 1.15 (0.26), residues: 413 sheet: -0.41 (0.34), residues: 212 loop : 0.25 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 161 TYR 0.013 0.001 TYR R 185 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6729 (mt-10) REVERT: B 186 ASP cc_start: 0.7778 (m-30) cc_final: 0.7509 (m-30) REVERT: N 5 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6611 (tm-30) REVERT: N 76 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7221 (ptpt) REVERT: N 120 GLN cc_start: 0.7331 (mm-40) cc_final: 0.7087 (mm-40) outliers start: 20 outliers final: 13 residues processed: 145 average time/residue: 2.5736 time to fit residues: 397.8083 Evaluate side-chains 143 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8430 Z= 0.238 Angle : 0.502 6.525 11413 Z= 0.276 Chirality : 0.039 0.144 1289 Planarity : 0.004 0.043 1451 Dihedral : 4.864 25.756 1172 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.81 % Allowed : 13.36 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1036 helix: 1.09 (0.26), residues: 412 sheet: -0.51 (0.33), residues: 214 loop : 0.18 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 99 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.002 PHE G 61 TYR 0.013 0.001 TYR R 185 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6842 (mt-10) REVERT: A 50 GLU cc_start: 0.5935 (pp20) cc_final: 0.5072 (mp0) REVERT: A 265 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6689 (tpm170) REVERT: A 390 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: B 186 ASP cc_start: 0.7727 (m-30) cc_final: 0.7503 (m-30) REVERT: G 19 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7166 (mp) REVERT: N 5 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: N 120 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7056 (mm-40) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 2.5672 time to fit residues: 390.8483 Evaluate side-chains 151 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8430 Z= 0.318 Angle : 0.539 6.592 11413 Z= 0.297 Chirality : 0.040 0.144 1289 Planarity : 0.005 0.058 1451 Dihedral : 5.144 25.239 1172 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.48 % Allowed : 13.36 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1036 helix: 0.92 (0.26), residues: 414 sheet: -0.68 (0.32), residues: 228 loop : 0.20 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 277 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.002 PHE G 61 TYR 0.015 0.002 TYR R 185 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6910 (mt-10) REVERT: A 390 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: G 19 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7262 (mp) REVERT: N 5 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: N 120 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7068 (mm-40) REVERT: R 13 VAL cc_start: 0.8646 (p) cc_final: 0.8446 (m) REVERT: R 117 MET cc_start: 0.6111 (tpp) cc_final: 0.5853 (tpp) outliers start: 31 outliers final: 19 residues processed: 145 average time/residue: 2.7615 time to fit residues: 424.6227 Evaluate side-chains 144 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8430 Z= 0.200 Angle : 0.494 5.736 11413 Z= 0.271 Chirality : 0.039 0.141 1289 Planarity : 0.004 0.045 1451 Dihedral : 4.834 26.201 1172 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.36 % Allowed : 14.93 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1036 helix: 1.02 (0.26), residues: 414 sheet: -0.65 (0.32), residues: 222 loop : 0.22 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS A 41 PHE 0.010 0.001 PHE R 175 TYR 0.011 0.001 TYR R 185 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6804 (mt-10) REVERT: A 50 GLU cc_start: 0.5777 (pp20) cc_final: 0.5103 (mp0) REVERT: A 390 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: G 14 LYS cc_start: 0.7578 (mtmt) cc_final: 0.6754 (mttp) REVERT: N 5 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: N 120 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7062 (mm-40) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 2.7731 time to fit residues: 409.3189 Evaluate side-chains 136 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8430 Z= 0.153 Angle : 0.472 5.777 11413 Z= 0.257 Chirality : 0.038 0.140 1289 Planarity : 0.004 0.050 1451 Dihedral : 4.594 27.030 1172 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.24 % Allowed : 15.60 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1036 helix: 1.12 (0.26), residues: 418 sheet: -0.58 (0.32), residues: 226 loop : 0.33 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS A 41 PHE 0.011 0.001 PHE G 61 TYR 0.011 0.001 TYR A 253 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6766 (mt-10) REVERT: A 50 GLU cc_start: 0.5700 (pp20) cc_final: 0.5048 (mp0) REVERT: A 390 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7170 (mt0) REVERT: G 14 LYS cc_start: 0.7577 (mtmt) cc_final: 0.6763 (mttp) REVERT: N 5 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: R 13 VAL cc_start: 0.8652 (p) cc_final: 0.8448 (m) REVERT: R 145 MET cc_start: 0.6164 (ptm) cc_final: 0.5963 (ptp) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 2.6360 time to fit residues: 400.2573 Evaluate side-chains 140 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8430 Z= 0.232 Angle : 0.499 5.357 11413 Z= 0.273 Chirality : 0.039 0.138 1289 Planarity : 0.004 0.051 1451 Dihedral : 4.807 26.245 1172 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.24 % Allowed : 15.71 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1036 helix: 1.06 (0.26), residues: 418 sheet: -0.63 (0.32), residues: 228 loop : 0.23 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 175 TYR 0.012 0.001 TYR R 185 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6856 (mt-10) REVERT: A 50 GLU cc_start: 0.5837 (pp20) cc_final: 0.5245 (mp0) REVERT: A 390 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: G 14 LYS cc_start: 0.7646 (mtmt) cc_final: 0.6828 (mttp) REVERT: N 5 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: R 13 VAL cc_start: 0.8637 (p) cc_final: 0.8403 (m) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 2.7157 time to fit residues: 400.8098 Evaluate side-chains 142 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8430 Z= 0.188 Angle : 0.487 5.434 11413 Z= 0.265 Chirality : 0.039 0.147 1289 Planarity : 0.004 0.061 1451 Dihedral : 4.708 26.873 1172 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.91 % Allowed : 16.05 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1036 helix: 1.06 (0.26), residues: 418 sheet: -0.61 (0.32), residues: 228 loop : 0.28 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.004 0.001 HIS A 41 PHE 0.010 0.001 PHE G 61 TYR 0.011 0.001 TYR R 185 ARG 0.009 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.5792 (pp20) cc_final: 0.5197 (mp0) REVERT: A 390 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: G 14 LYS cc_start: 0.7639 (mtmt) cc_final: 0.6827 (mttp) REVERT: N 5 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: R 13 VAL cc_start: 0.8631 (p) cc_final: 0.8406 (m) REVERT: R 120 PHE cc_start: 0.7268 (t80) cc_final: 0.7007 (t80) outliers start: 17 outliers final: 15 residues processed: 139 average time/residue: 2.6623 time to fit residues: 393.7563 Evaluate side-chains 138 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 254 CYS Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113686 restraints weight = 26205.869| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.57 r_work: 0.3079 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8430 Z= 0.149 Angle : 0.469 5.311 11413 Z= 0.255 Chirality : 0.038 0.142 1289 Planarity : 0.004 0.062 1451 Dihedral : 4.504 27.325 1172 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.13 % Allowed : 15.94 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1036 helix: 1.20 (0.26), residues: 419 sheet: -0.56 (0.33), residues: 222 loop : 0.24 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS A 41 PHE 0.013 0.001 PHE R 175 TYR 0.009 0.001 TYR R 185 ARG 0.010 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.31 seconds wall clock time: 127 minutes 20.37 seconds (7640.37 seconds total)