Starting phenix.real_space_refine on Wed Feb 14 07:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia8_35298/02_2024/8ia8_35298_neut.pdb" } resolution = 2.86 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5620 2.51 5 N 1506 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 16": "NH1" <-> "NH2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8810 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 56 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2255 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1716 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2580 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.01, per 1000 atoms: 0.57 Number of scatterers: 8810 At special positions: 0 Unit cell: (91.8, 123.25, 125.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1616 8.00 N 1506 7.00 C 5620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 2.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 15 sheets defined 35.9% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 20 through 51 removed outlier: 3.745A pdb=" N SER A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.540A pdb=" N SER A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.946A pdb=" N SER A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.547A pdb=" N ILE A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.573A pdb=" N ALA A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 147 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 345 through 363 removed outlier: 3.653A pdb=" N ILE A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 359 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.541A pdb=" N HIS A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.731A pdb=" N CYS A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 440 through 454 Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.800A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.077A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.515A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.664A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 removed outlier: 3.680A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.604A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.753A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.508A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.613A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 191 removed outlier: 6.161A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ALA C 220 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.558A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.780A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.983A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.604A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.755A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.563A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.722A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.409A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.678A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.678A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2822 1.34 - 1.46: 2081 1.46 - 1.58: 3998 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 8997 Sorted by residual: bond pdb=" C PRO A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.51e-02 4.39e+03 2.33e+00 bond pdb=" C VAL S 2 " pdb=" O VAL S 2 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.19e-02 7.06e+03 1.99e+00 bond pdb=" C ILE A 116 " pdb=" O ILE A 116 " ideal model delta sigma weight residual 1.239 1.224 0.015 1.13e-02 7.83e+03 1.82e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.334 1.364 -0.031 2.34e-02 1.83e+03 1.71e+00 bond pdb=" C MET A 138 " pdb=" N ALA A 139 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.31e-02 5.83e+03 1.52e+00 ... (remaining 8992 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.55: 209 106.55 - 113.43: 4938 113.43 - 120.31: 3316 120.31 - 127.20: 3629 127.20 - 134.08: 98 Bond angle restraints: 12190 Sorted by residual: angle pdb=" N GLY L 13 " pdb=" CA GLY L 13 " pdb=" C GLY L 13 " ideal model delta sigma weight residual 112.60 106.66 5.94 1.53e+00 4.27e-01 1.51e+01 angle pdb=" N SER A 117 " pdb=" CA SER A 117 " pdb=" C SER A 117 " ideal model delta sigma weight residual 113.88 109.22 4.66 1.23e+00 6.61e-01 1.43e+01 angle pdb=" CA GLY L 13 " pdb=" C GLY L 13 " pdb=" N LEU L 14 " ideal model delta sigma weight residual 114.78 118.92 -4.14 1.16e+00 7.43e-01 1.27e+01 angle pdb=" N CYS A 95 " pdb=" CA CYS A 95 " pdb=" C CYS A 95 " ideal model delta sigma weight residual 112.72 108.02 4.70 1.36e+00 5.41e-01 1.19e+01 angle pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N SER B 331 " ideal model delta sigma weight residual 114.74 118.43 -3.69 1.13e+00 7.83e-01 1.07e+01 ... (remaining 12185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 4692 14.14 - 28.29: 479 28.29 - 42.43: 121 42.43 - 56.57: 27 56.57 - 70.72: 8 Dihedral angle restraints: 5327 sinusoidal: 2054 harmonic: 3273 Sorted by residual: dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N ARG B 52 " pdb=" CA ARG B 52 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 770 0.031 - 0.062: 409 0.062 - 0.093: 136 0.093 - 0.125: 67 0.125 - 0.156: 8 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU A 75 " pdb=" CB LEU A 75 " pdb=" CD1 LEU A 75 " pdb=" CD2 LEU A 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB THR S 91 " pdb=" CA THR S 91 " pdb=" OG1 THR S 91 " pdb=" CG2 THR S 91 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1387 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 287 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO C 288 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 21 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 22 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO S 75 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.031 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 217 2.70 - 3.25: 8268 3.25 - 3.80: 12831 3.80 - 4.35: 17619 4.35 - 4.90: 30675 Nonbonded interactions: 69610 Sorted by model distance: nonbonded pdb=" O GLY C 45 " pdb=" OG1 THR C 48 " model vdw 2.148 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.155 2.440 nonbonded pdb=" O LEU A 387 " pdb=" OG1 THR A 391 " model vdw 2.185 2.440 nonbonded pdb=" O VAL A 23 " pdb=" OG SER A 26 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG L 16 " pdb=" O TYR A 393 " model vdw 2.227 2.520 ... (remaining 69605 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: 2.290 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: 0.010 Extract box with map and model: 7.080 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.005 0.040 8997 Z= 0.332 Angle : 0.632 6.920 12190 Z= 0.363 Chirality : 0.045 0.156 1390 Planarity : 0.004 0.078 1537 Dihedral : 12.725 70.718 3206 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.42 % Allowed : 0.21 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -1.21 (0.24), residues: 1114 helix: -0.34 (0.27), residues: 375 sheet: -0.21 (0.32), residues: 280 loop : -1.48 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.002 PHE A 164 TYR 0.014 0.001 TYR B 105 ARG 0.005 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.086 Fit side-chains REVERT: S 1 ASP cc_start: 0.7641 (t70) cc_final: 0.7426 (t70) outliers start: 4 outliers final: 0 residues processed: 144 average time/residue: 1.7219 time to fit residues: 259.6333 Evaluate side-chains 111 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 88 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8997 Z= 0.212 Angle : 0.579 6.825 12190 Z= 0.305 Chirality : 0.044 0.324 1390 Planarity : 0.004 0.063 1537 Dihedral : 4.505 24.767 1218 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.67 % Allowed : 9.41 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1114 helix: 0.56 (0.28), residues: 380 sheet: 0.02 (0.31), residues: 288 loop : -1.36 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE S 29 TYR 0.015 0.001 TYR S 190 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.054 Fit side-chains REVERT: C 245 GLU cc_start: 0.7566 (mp0) cc_final: 0.7328 (mp0) REVERT: C 330 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (mtpt) REVERT: S 1 ASP cc_start: 0.7521 (t70) cc_final: 0.7224 (t0) outliers start: 16 outliers final: 7 residues processed: 129 average time/residue: 1.6169 time to fit residues: 219.3173 Evaluate side-chains 117 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8997 Z= 0.150 Angle : 0.520 8.318 12190 Z= 0.273 Chirality : 0.043 0.308 1390 Planarity : 0.004 0.064 1537 Dihedral : 4.146 21.589 1218 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 10.88 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.08 (0.25), residues: 1114 helix: 1.15 (0.28), residues: 376 sheet: 0.15 (0.31), residues: 286 loop : -1.19 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE A 34 TYR 0.013 0.001 TYR S 190 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.011 Fit side-chains REVERT: A 84 LEU cc_start: 0.8165 (mt) cc_final: 0.7797 (tp) REVERT: A 155 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 352 MET cc_start: 0.8909 (mtp) cc_final: 0.8541 (mtp) REVERT: A 365 ARG cc_start: 0.7597 (ptm160) cc_final: 0.7340 (ptp-110) REVERT: C 242 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.8090 (ttm-80) REVERT: C 245 GLU cc_start: 0.7563 (mp0) cc_final: 0.7227 (mp0) REVERT: B 23 LYS cc_start: 0.8795 (tttp) cc_final: 0.8441 (tppt) REVERT: B 198 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8494 (pp) REVERT: G 42 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7565 (mm-30) REVERT: G 58 GLU cc_start: 0.8565 (pm20) cc_final: 0.8188 (pm20) REVERT: S 1 ASP cc_start: 0.7433 (t70) cc_final: 0.7077 (t0) outliers start: 21 outliers final: 6 residues processed: 131 average time/residue: 1.5150 time to fit residues: 209.1662 Evaluate side-chains 119 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8997 Z= 0.173 Angle : 0.523 7.890 12190 Z= 0.274 Chirality : 0.042 0.244 1390 Planarity : 0.004 0.062 1537 Dihedral : 4.045 21.623 1218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.20 % Allowed : 12.66 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.15 (0.25), residues: 1114 helix: 1.41 (0.29), residues: 376 sheet: 0.23 (0.31), residues: 288 loop : -1.09 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 34 TYR 0.012 0.001 TYR S 190 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.123 Fit side-chains REVERT: A 84 LEU cc_start: 0.8165 (mt) cc_final: 0.7800 (tp) REVERT: A 155 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7283 (mp) REVERT: A 352 MET cc_start: 0.8897 (mtp) cc_final: 0.8540 (mtp) REVERT: A 365 ARG cc_start: 0.7627 (ptm160) cc_final: 0.7386 (ptp-110) REVERT: C 242 ARG cc_start: 0.8371 (ttp-170) cc_final: 0.8111 (ttm-80) REVERT: C 245 GLU cc_start: 0.7590 (mp0) cc_final: 0.7185 (mp0) REVERT: B 19 ARG cc_start: 0.8463 (tmm160) cc_final: 0.8260 (tmm160) REVERT: B 23 LYS cc_start: 0.8726 (tttp) cc_final: 0.8332 (tppt) REVERT: B 198 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8477 (pp) REVERT: G 58 GLU cc_start: 0.8573 (pm20) cc_final: 0.8160 (pm20) outliers start: 21 outliers final: 10 residues processed: 122 average time/residue: 1.6257 time to fit residues: 208.6406 Evaluate side-chains 123 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8997 Z= 0.213 Angle : 0.533 8.229 12190 Z= 0.280 Chirality : 0.043 0.212 1390 Planarity : 0.004 0.040 1537 Dihedral : 4.078 22.782 1218 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.03 % Allowed : 12.76 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1114 helix: 1.50 (0.29), residues: 377 sheet: 0.28 (0.31), residues: 288 loop : -1.11 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 107 TYR 0.012 0.001 TYR B 105 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.987 Fit side-chains REVERT: A 84 LEU cc_start: 0.8108 (mt) cc_final: 0.7750 (tp) REVERT: A 155 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 352 MET cc_start: 0.8919 (mtp) cc_final: 0.8564 (mtp) REVERT: A 365 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7360 (ptp-110) REVERT: C 245 GLU cc_start: 0.7590 (mp0) cc_final: 0.7195 (mp0) REVERT: B 23 LYS cc_start: 0.8712 (tttp) cc_final: 0.8331 (tppt) REVERT: B 198 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8477 (pp) REVERT: G 58 GLU cc_start: 0.8575 (pm20) cc_final: 0.8155 (pm20) outliers start: 29 outliers final: 14 residues processed: 124 average time/residue: 1.4901 time to fit residues: 194.7558 Evaluate side-chains 125 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8997 Z= 0.213 Angle : 0.535 8.331 12190 Z= 0.279 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.044 1537 Dihedral : 4.071 22.807 1218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.51 % Allowed : 13.81 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.28 (0.26), residues: 1114 helix: 1.55 (0.29), residues: 378 sheet: 0.28 (0.31), residues: 288 loop : -1.06 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.009 0.001 PHE B 151 TYR 0.012 0.001 TYR C 230 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.928 Fit side-chains REVERT: A 84 LEU cc_start: 0.8260 (mt) cc_final: 0.7862 (tp) REVERT: A 155 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7369 (mp) REVERT: A 352 MET cc_start: 0.8922 (mtp) cc_final: 0.8595 (mtp) REVERT: C 242 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.8161 (ttm-80) REVERT: C 245 GLU cc_start: 0.7623 (mp0) cc_final: 0.7199 (mp0) REVERT: B 23 LYS cc_start: 0.8690 (tttp) cc_final: 0.8328 (tppt) REVERT: B 46 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7137 (mmp80) REVERT: B 198 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8457 (pp) REVERT: B 215 GLU cc_start: 0.7992 (mp0) cc_final: 0.7433 (mp0) REVERT: G 58 GLU cc_start: 0.8582 (pm20) cc_final: 0.8140 (pm20) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 1.5522 time to fit residues: 204.4316 Evaluate side-chains 124 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8997 Z= 0.200 Angle : 0.533 8.631 12190 Z= 0.278 Chirality : 0.042 0.166 1390 Planarity : 0.004 0.056 1537 Dihedral : 4.037 22.469 1218 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 14.44 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.34 (0.26), residues: 1114 helix: 1.63 (0.28), residues: 378 sheet: 0.30 (0.31), residues: 288 loop : -1.02 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 107 TYR 0.012 0.001 TYR C 230 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.019 Fit side-chains REVERT: A 84 LEU cc_start: 0.8306 (mt) cc_final: 0.7900 (tp) REVERT: A 155 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7411 (mp) REVERT: A 352 MET cc_start: 0.8920 (mtp) cc_final: 0.8604 (mtp) REVERT: C 242 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.8196 (ttm-80) REVERT: C 245 GLU cc_start: 0.7636 (mp0) cc_final: 0.7198 (mp0) REVERT: B 23 LYS cc_start: 0.8669 (tttp) cc_final: 0.8317 (tppt) REVERT: B 46 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7175 (mmp80) REVERT: B 198 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8452 (pp) REVERT: B 215 GLU cc_start: 0.7994 (mp0) cc_final: 0.7478 (mp0) REVERT: G 58 GLU cc_start: 0.8579 (pm20) cc_final: 0.8141 (pm20) outliers start: 25 outliers final: 15 residues processed: 124 average time/residue: 1.6448 time to fit residues: 214.4851 Evaluate side-chains 128 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8997 Z= 0.164 Angle : 0.520 8.863 12190 Z= 0.270 Chirality : 0.041 0.137 1390 Planarity : 0.004 0.064 1537 Dihedral : 3.931 21.000 1218 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 15.27 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1114 helix: 1.72 (0.28), residues: 380 sheet: 0.42 (0.32), residues: 279 loop : -0.99 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS S 35 PHE 0.009 0.001 PHE A 107 TYR 0.012 0.001 TYR C 230 ARG 0.013 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.126 Fit side-chains REVERT: A 84 LEU cc_start: 0.8306 (mt) cc_final: 0.7906 (tp) REVERT: A 155 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 352 MET cc_start: 0.8896 (mtp) cc_final: 0.8610 (mtp) REVERT: C 245 GLU cc_start: 0.7654 (mp0) cc_final: 0.7193 (mp0) REVERT: B 23 LYS cc_start: 0.8658 (tttp) cc_final: 0.8304 (tppt) REVERT: B 46 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7145 (mmp80) REVERT: B 198 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 215 GLU cc_start: 0.7985 (mp0) cc_final: 0.7470 (mp0) REVERT: G 58 GLU cc_start: 0.8574 (pm20) cc_final: 0.8141 (pm20) outliers start: 21 outliers final: 11 residues processed: 125 average time/residue: 1.5923 time to fit residues: 209.3037 Evaluate side-chains 124 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8997 Z= 0.258 Angle : 0.558 9.024 12190 Z= 0.291 Chirality : 0.043 0.138 1390 Planarity : 0.004 0.055 1537 Dihedral : 4.095 23.660 1218 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.30 % Allowed : 15.79 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.36 (0.25), residues: 1114 helix: 1.65 (0.28), residues: 380 sheet: 0.38 (0.32), residues: 279 loop : -1.06 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR B 105 ARG 0.014 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.092 Fit side-chains REVERT: A 84 LEU cc_start: 0.8316 (mt) cc_final: 0.7907 (tp) REVERT: A 155 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7472 (mp) REVERT: A 352 MET cc_start: 0.8914 (mtp) cc_final: 0.8569 (mtp) REVERT: C 24 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6852 (mtt90) REVERT: C 245 GLU cc_start: 0.7644 (mp0) cc_final: 0.7287 (mp0) REVERT: B 23 LYS cc_start: 0.8668 (tttp) cc_final: 0.8316 (tppt) REVERT: B 46 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7183 (mmp80) REVERT: B 198 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8442 (pp) REVERT: B 215 GLU cc_start: 0.7995 (mp0) cc_final: 0.7477 (mp0) REVERT: G 58 GLU cc_start: 0.8568 (pm20) cc_final: 0.8139 (pm20) REVERT: S 39 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8351 (tt0) outliers start: 22 outliers final: 11 residues processed: 122 average time/residue: 1.6531 time to fit residues: 211.8993 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8997 Z= 0.229 Angle : 0.549 9.066 12190 Z= 0.286 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.055 1537 Dihedral : 4.108 23.490 1218 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.25), residues: 1114 helix: 1.70 (0.28), residues: 380 sheet: 0.42 (0.32), residues: 279 loop : -1.05 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 164 TYR 0.011 0.001 TYR C 230 ARG 0.015 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.068 Fit side-chains REVERT: A 84 LEU cc_start: 0.8315 (mt) cc_final: 0.7900 (tp) REVERT: A 155 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 352 MET cc_start: 0.8908 (mtp) cc_final: 0.8570 (mtp) REVERT: C 245 GLU cc_start: 0.7640 (mp0) cc_final: 0.7285 (mp0) REVERT: B 23 LYS cc_start: 0.8668 (tttp) cc_final: 0.8313 (tppt) REVERT: B 198 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8464 (pp) REVERT: B 215 GLU cc_start: 0.7998 (mp0) cc_final: 0.7481 (mp0) REVERT: G 58 GLU cc_start: 0.8571 (pm20) cc_final: 0.8137 (pm20) REVERT: S 39 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8376 (tt0) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 1.6243 time to fit residues: 208.0706 Evaluate side-chains 127 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086500 restraints weight = 11298.557| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.52 r_work: 0.2775 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8997 Z= 0.199 Angle : 0.538 9.048 12190 Z= 0.280 Chirality : 0.042 0.138 1390 Planarity : 0.004 0.057 1537 Dihedral : 4.053 22.674 1218 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1114 helix: 1.76 (0.28), residues: 381 sheet: 0.49 (0.32), residues: 278 loop : -1.04 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 164 TYR 0.011 0.001 TYR S 190 ARG 0.014 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.57 seconds wall clock time: 69 minutes 33.77 seconds (4173.77 seconds total)