Starting phenix.real_space_refine on Mon Mar 11 18:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8guq_34276/03_2024/8guq_34276_neut_updated.pdb" } resolution = 3.08 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= -0.001 sd= 0.042 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 66 5.16 5 C 5602 2.51 5 N 1499 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 147": "NH1" <-> "NH2" Residue "R ARG 149": "NH1" <-> "NH2" Residue "R GLU 181": "OE1" <-> "OE2" Residue "R ASP 189": "OD1" <-> "OD2" Residue "R ARG 242": "NH1" <-> "NH2" Residue "R GLU 305": "OE1" <-> "OE2" Residue "R ARG 307": "NH1" <-> "NH2" Residue "S ARG 98": "NH1" <-> "NH2" Residue "S ASP 125": "OD1" <-> "OD2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S ASP 189": "OD1" <-> "OD2" Residue "S ARG 206": "NH1" <-> "NH2" Residue "S GLU 210": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8789 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1721 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'KNF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.59 Number of scatterers: 8789 At special positions: 0 Unit cell: (90.1334, 116.48, 131.733, 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 66 16.00 O 1622 8.00 N 1499 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 15 sheets defined 32.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.708A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.506A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.943A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.533A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.850A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.942A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.949A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.542A pdb=" N ARG C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.502A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.614A pdb=" N LEU R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 95 removed outlier: 3.886A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN R 93 " --> pdb=" O CYS R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 133 removed outlier: 3.712A pdb=" N VAL R 113 " --> pdb=" O LYS R 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER R 120 " --> pdb=" O THR R 116 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 165 removed outlier: 3.602A pdb=" N VAL R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR R 153 " --> pdb=" O ARG R 149 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 160 " --> pdb=" O ILE R 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 223 removed outlier: 3.702A pdb=" N LEU R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR R 208 " --> pdb=" O GLY R 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS R 217 " --> pdb=" O LEU R 213 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS R 219 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 270 removed outlier: 3.665A pdb=" N THR R 246 " --> pdb=" O ARG R 242 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N CYS R 257 " --> pdb=" O VAL R 253 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE R 259 " --> pdb=" O LEU R 255 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 4.246A pdb=" N LEU R 264 " --> pdb=" O PRO R 260 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU R 269 " --> pdb=" O MET R 265 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 298 removed outlier: 3.727A pdb=" N ALA R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE R 283 " --> pdb=" O LYS R 279 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS R 288 " --> pdb=" O CYS R 284 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER R 292 " --> pdb=" O CYS R 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN R 295 " --> pdb=" O ASN R 291 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.518A pdb=" N HIS R 311 " --> pdb=" O ARG R 307 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU R 314 " --> pdb=" O ALA R 310 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA R 315 " --> pdb=" O HIS R 311 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS R 316 " --> pdb=" O HIS R 312 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.656A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.639A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.911A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.928A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.648A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.565A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.827A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.423A 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: 5.032A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.431A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.734A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.506A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.518A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 95 through 97 removed outlier: 6.058A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.606A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= O, first strand: chain 'S' and resid 213 through 219 removed outlier: 6.159A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 933 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: 2.45 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2819 1.35 - 1.47: 2323 1.47 - 1.60: 3740 1.60 - 1.73: 0 1.73 - 1.86: 95 Bond restraints: 8977 Sorted by residual: bond pdb=" C10 KNF R 401 " pdb=" C6 KNF R 401 " ideal model delta sigma weight residual 1.587 1.359 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C11 KNF R 401 " pdb=" C5 KNF R 401 " ideal model delta sigma weight residual 1.549 1.342 0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C11 KNF R 401 " pdb=" N5 KNF R 401 " ideal model delta sigma weight residual 1.477 1.339 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" N1 KNF R 401 " pdb=" O1 KNF R 401 " ideal model delta sigma weight residual 1.406 1.275 0.131 2.00e-02 2.50e+03 4.26e+01 bond pdb=" C3 KNF R 401 " pdb=" N3 KNF R 401 " ideal model delta sigma weight residual 1.466 1.341 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 8972 not shown) Histogram of bond angle deviations from ideal: 59.56 - 76.95: 3 76.95 - 94.35: 2 94.35 - 111.75: 4207 111.75 - 129.15: 7874 129.15 - 146.55: 82 Bond angle restraints: 12168 Sorted by residual: angle pdb=" C10 KNF R 401 " pdb=" C9 KNF R 401 " pdb=" C18 KNF R 401 " ideal model delta sigma weight residual 127.55 93.72 33.83 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C7 KNF R 401 " pdb=" C8 KNF R 401 " pdb=" C9 KNF R 401 " ideal model delta sigma weight residual 107.86 89.39 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 122.08 129.35 -7.27 1.47e+00 4.63e-01 2.45e+01 angle pdb=" C SER R 61 " pdb=" N HIS R 62 " pdb=" CA HIS R 62 " ideal model delta sigma weight residual 122.08 129.33 -7.25 1.47e+00 4.63e-01 2.43e+01 angle pdb=" CA CYS R 174 " pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " ideal model delta sigma weight residual 114.40 124.73 -10.33 2.30e+00 1.89e-01 2.02e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4694 17.53 - 35.05: 499 35.05 - 52.58: 96 52.58 - 70.10: 17 70.10 - 87.63: 5 Dihedral angle restraints: 5311 sinusoidal: 2027 harmonic: 3284 Sorted by residual: dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 -133.22 -46.78 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual 93.00 21.31 71.69 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CA HIS R 62 " pdb=" C HIS R 62 " pdb=" N GLN R 63 " pdb=" CA GLN R 63 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1244 0.090 - 0.180: 133 0.180 - 0.270: 13 0.270 - 0.359: 0 0.359 - 0.449: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C9 KNF R 401 " pdb=" C10 KNF R 401 " pdb=" C18 KNF R 401 " pdb=" C8 KNF R 401 " both_signs ideal model delta sigma weight residual True 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 1388 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO S 173 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 173 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C THR R 173 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 173 " 0.017 2.00e-02 2.50e+03 pdb=" N CYS R 174 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 259 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO R 260 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 260 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 260 " -0.035 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1966 2.77 - 3.30: 7652 3.30 - 3.84: 14467 3.84 - 4.37: 17713 4.37 - 4.90: 30851 Nonbonded interactions: 72649 Sorted by model distance: nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.265 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.268 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.278 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 2.440 ... (remaining 72644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.070 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.510 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.228 8977 Z= 0.664 Angle : 1.010 33.831 12168 Z= 0.511 Chirality : 0.057 0.449 1391 Planarity : 0.006 0.066 1525 Dihedral : 14.889 87.628 3184 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.32 % Allowed : 8.47 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.16 (0.19), residues: 1117 helix: -4.53 (0.11), residues: 379 sheet: -2.72 (0.27), residues: 269 loop : -2.63 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 63 HIS 0.009 0.002 HIS B 142 PHE 0.026 0.003 PHE S 27 TYR 0.037 0.003 TYR S 178 ARG 0.010 0.001 ARG R 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7478 (tp30) REVERT: A 270 LYS cc_start: 0.7873 (mttt) cc_final: 0.7184 (mmtm) REVERT: A 272 ASP cc_start: 0.7245 (m-30) cc_final: 0.6985 (p0) REVERT: A 304 GLN cc_start: 0.7792 (tt0) cc_final: 0.7318 (tt0) REVERT: A 331 ASN cc_start: 0.8276 (m-40) cc_final: 0.8042 (m110) REVERT: A 346 ASN cc_start: 0.8438 (m-40) cc_final: 0.8047 (m-40) REVERT: B 59 TYR cc_start: 0.8484 (m-80) cc_final: 0.7793 (m-80) REVERT: B 232 ILE cc_start: 0.8415 (tt) cc_final: 0.7988 (tt) REVERT: B 243 THR cc_start: 0.8717 (p) cc_final: 0.8363 (p) REVERT: B 317 CYS cc_start: 0.7653 (p) cc_final: 0.7325 (p) REVERT: B 335 PHE cc_start: 0.8278 (m-80) cc_final: 0.8077 (m-10) REVERT: R 43 LEU cc_start: 0.8240 (mt) cc_final: 0.8018 (mt) REVERT: R 302 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7492 (mmt90) REVERT: S 18 ARG cc_start: 0.7166 (tpp80) cc_final: 0.6933 (tpt170) REVERT: S 46 GLU cc_start: 0.7783 (pt0) cc_final: 0.7510 (pt0) REVERT: S 60 TYR cc_start: 0.8851 (m-80) cc_final: 0.8647 (m-80) REVERT: S 190 ARG cc_start: 0.8206 (ptt-90) cc_final: 0.7996 (ptt90) REVERT: S 198 THR cc_start: 0.7526 (t) cc_final: 0.6985 (m) outliers start: 3 outliers final: 1 residues processed: 186 average time/residue: 0.2556 time to fit residues: 61.7481 Evaluate side-chains 158 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 213 HIS A 255 ASN B 62 HIS B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 218 GLN R 291 ASN R 316 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8977 Z= 0.192 Angle : 0.596 12.274 12168 Z= 0.303 Chirality : 0.041 0.141 1391 Planarity : 0.004 0.046 1525 Dihedral : 5.765 56.454 1229 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.48 % Allowed : 13.44 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.66 (0.21), residues: 1117 helix: -2.67 (0.20), residues: 381 sheet: -2.12 (0.29), residues: 258 loop : -2.20 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.002 0.001 HIS B 225 PHE 0.015 0.002 PHE A 189 TYR 0.023 0.001 TYR A 296 ARG 0.006 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8067 (tpp) cc_final: 0.7652 (tpp) REVERT: A 270 LYS cc_start: 0.7827 (mttt) cc_final: 0.7088 (mmtm) REVERT: A 272 ASP cc_start: 0.7594 (m-30) cc_final: 0.7369 (p0) REVERT: A 304 GLN cc_start: 0.7693 (tt0) cc_final: 0.7272 (tt0) REVERT: A 341 ASP cc_start: 0.7309 (t0) cc_final: 0.7093 (t0) REVERT: A 346 ASN cc_start: 0.8567 (m-40) cc_final: 0.8251 (m-40) REVERT: B 59 TYR cc_start: 0.8516 (m-80) cc_final: 0.7910 (m-80) REVERT: B 232 ILE cc_start: 0.8355 (tt) cc_final: 0.7974 (tt) REVERT: B 243 THR cc_start: 0.8157 (p) cc_final: 0.7730 (p) REVERT: B 317 CYS cc_start: 0.7407 (p) cc_final: 0.7153 (p) REVERT: C 13 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6776 (ttm110) REVERT: R 22 MET cc_start: 0.8164 (tpp) cc_final: 0.7712 (tpp) REVERT: R 51 ASN cc_start: 0.7638 (m-40) cc_final: 0.7371 (m110) REVERT: R 302 ARG cc_start: 0.7821 (tpp-160) cc_final: 0.7522 (mmt90) REVERT: S 18 ARG cc_start: 0.7258 (tpp80) cc_final: 0.7024 (tpt170) outliers start: 14 outliers final: 12 residues processed: 176 average time/residue: 0.2324 time to fit residues: 54.8133 Evaluate side-chains 167 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.0050 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8977 Z= 0.197 Angle : 0.558 11.198 12168 Z= 0.281 Chirality : 0.041 0.143 1391 Planarity : 0.003 0.045 1525 Dihedral : 5.394 52.670 1229 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.22 % Allowed : 15.13 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.74 (0.23), residues: 1117 helix: -1.32 (0.24), residues: 377 sheet: -2.00 (0.29), residues: 260 loop : -1.97 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS S 35 PHE 0.016 0.002 PHE A 189 TYR 0.026 0.001 TYR S 178 ARG 0.003 0.000 ARG R 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7964 (mttt) cc_final: 0.7261 (mmtm) REVERT: A 304 GLN cc_start: 0.7726 (tt0) cc_final: 0.7238 (tt0) REVERT: A 346 ASN cc_start: 0.8446 (m-40) cc_final: 0.8147 (m-40) REVERT: B 52 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7745 (mpt180) REVERT: B 59 TYR cc_start: 0.8473 (m-80) cc_final: 0.8098 (m-80) REVERT: B 232 ILE cc_start: 0.8367 (tt) cc_final: 0.7987 (tt) REVERT: B 234 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: B 243 THR cc_start: 0.8018 (p) cc_final: 0.7576 (p) REVERT: B 317 CYS cc_start: 0.7411 (p) cc_final: 0.7150 (p) REVERT: C 13 ARG cc_start: 0.7028 (ttm110) cc_final: 0.6715 (ttm110) REVERT: R 27 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5383 (mm) REVERT: R 51 ASN cc_start: 0.7659 (m-40) cc_final: 0.7401 (m110) REVERT: R 157 MET cc_start: 0.8088 (tmm) cc_final: 0.7741 (tmm) REVERT: R 286 MET cc_start: 0.7096 (mmm) cc_final: 0.6606 (mmm) REVERT: R 302 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7505 (mmt90) REVERT: S 21 SER cc_start: 0.7888 (t) cc_final: 0.7085 (p) REVERT: S 113 GLN cc_start: 0.7687 (mm110) cc_final: 0.7485 (mm-40) outliers start: 21 outliers final: 13 residues processed: 181 average time/residue: 0.2378 time to fit residues: 57.3560 Evaluate side-chains 165 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 244 HIS A 306 GLN B 183 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8977 Z= 0.323 Angle : 0.608 14.020 12168 Z= 0.305 Chirality : 0.044 0.148 1391 Planarity : 0.004 0.043 1525 Dihedral : 5.462 50.734 1229 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.92 % Allowed : 17.04 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.30 (0.23), residues: 1117 helix: -0.58 (0.26), residues: 377 sheet: -2.12 (0.28), residues: 265 loop : -1.80 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.004 0.001 HIS B 142 PHE 0.022 0.002 PHE A 189 TYR 0.029 0.002 TYR S 178 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 182 THR cc_start: 0.6571 (m) cc_final: 0.6289 (t) REVERT: A 270 LYS cc_start: 0.7820 (mttt) cc_final: 0.7102 (mmtm) REVERT: A 304 GLN cc_start: 0.7717 (tt0) cc_final: 0.7306 (tt0) REVERT: B 59 TYR cc_start: 0.8512 (m-80) cc_final: 0.8250 (m-80) REVERT: B 232 ILE cc_start: 0.8426 (tt) cc_final: 0.8004 (tt) REVERT: B 234 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: B 243 THR cc_start: 0.7975 (p) cc_final: 0.7596 (p) REVERT: B 317 CYS cc_start: 0.7532 (p) cc_final: 0.7271 (p) REVERT: C 13 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6702 (ttm110) REVERT: R 70 TYR cc_start: 0.9065 (m-80) cc_final: 0.8591 (m-80) REVERT: R 157 MET cc_start: 0.8172 (tmm) cc_final: 0.7700 (tmm) REVERT: R 170 MET cc_start: 0.6335 (mpp) cc_final: 0.5736 (pmm) REVERT: R 302 ARG cc_start: 0.7715 (tpp-160) cc_final: 0.7392 (mmt90) REVERT: S 21 SER cc_start: 0.7994 (t) cc_final: 0.7269 (p) REVERT: S 83 MET cc_start: 0.8034 (ptp) cc_final: 0.7731 (ptp) REVERT: S 128 MET cc_start: 0.8202 (mmm) cc_final: 0.7412 (mmm) REVERT: S 212 VAL cc_start: 0.9036 (t) cc_final: 0.8620 (m) outliers start: 37 outliers final: 26 residues processed: 176 average time/residue: 0.2428 time to fit residues: 57.6637 Evaluate side-chains 172 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8977 Z= 0.184 Angle : 0.561 12.584 12168 Z= 0.276 Chirality : 0.041 0.148 1391 Planarity : 0.003 0.042 1525 Dihedral : 5.166 46.286 1229 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.54 % Allowed : 19.05 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.88 (0.24), residues: 1117 helix: -0.19 (0.26), residues: 388 sheet: -1.82 (0.29), residues: 257 loop : -1.70 (0.27), residues: 472 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 0.019 0.001 PHE A 189 TYR 0.025 0.001 TYR S 178 ARG 0.002 0.000 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6543 (m) cc_final: 0.6198 (t) REVERT: A 270 LYS cc_start: 0.7894 (mttt) cc_final: 0.7212 (mmtm) REVERT: A 304 GLN cc_start: 0.7727 (tt0) cc_final: 0.7292 (tt0) REVERT: B 188 MET cc_start: 0.7400 (mmm) cc_final: 0.7032 (mmm) REVERT: B 232 ILE cc_start: 0.8391 (tt) cc_final: 0.8002 (tt) REVERT: B 234 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: B 243 THR cc_start: 0.7994 (p) cc_final: 0.7611 (p) REVERT: B 262 MET cc_start: 0.7464 (ttm) cc_final: 0.7166 (ttm) REVERT: B 317 CYS cc_start: 0.7449 (p) cc_final: 0.6936 (t) REVERT: B 335 PHE cc_start: 0.8353 (m-80) cc_final: 0.8107 (m-10) REVERT: C 13 ARG cc_start: 0.7064 (ttm110) cc_final: 0.6727 (ttm110) REVERT: R 157 MET cc_start: 0.8141 (tmm) cc_final: 0.7600 (tmm) REVERT: R 170 MET cc_start: 0.6410 (mpp) cc_final: 0.5892 (pmm) REVERT: R 286 MET cc_start: 0.7164 (mmm) cc_final: 0.6838 (mmm) REVERT: R 302 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.7380 (mmt90) REVERT: S 21 SER cc_start: 0.7822 (t) cc_final: 0.7070 (p) REVERT: S 113 GLN cc_start: 0.7605 (mm110) cc_final: 0.7337 (mm-40) REVERT: S 128 MET cc_start: 0.8146 (mmm) cc_final: 0.7466 (mmm) REVERT: S 212 VAL cc_start: 0.8941 (t) cc_final: 0.8547 (m) outliers start: 24 outliers final: 17 residues processed: 175 average time/residue: 0.2264 time to fit residues: 53.3732 Evaluate side-chains 169 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 218 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8977 Z= 0.209 Angle : 0.552 13.656 12168 Z= 0.275 Chirality : 0.042 0.168 1391 Planarity : 0.003 0.042 1525 Dihedral : 5.057 41.431 1229 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.07 % Allowed : 18.94 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.67 (0.24), residues: 1117 helix: 0.01 (0.26), residues: 394 sheet: -1.75 (0.29), residues: 262 loop : -1.57 (0.28), residues: 461 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 0.024 0.002 PHE A 189 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG R 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6678 (m) cc_final: 0.6289 (t) REVERT: A 270 LYS cc_start: 0.7914 (mttt) cc_final: 0.7218 (mmtm) REVERT: A 304 GLN cc_start: 0.7732 (tt0) cc_final: 0.7301 (tt0) REVERT: B 20 ASP cc_start: 0.6510 (m-30) cc_final: 0.6178 (m-30) REVERT: B 52 ARG cc_start: 0.8015 (mpt180) cc_final: 0.7756 (mpt180) REVERT: B 188 MET cc_start: 0.7453 (mmm) cc_final: 0.7071 (mmm) REVERT: B 232 ILE cc_start: 0.8377 (tt) cc_final: 0.7975 (tt) REVERT: B 234 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: B 243 THR cc_start: 0.7913 (p) cc_final: 0.7579 (p) REVERT: B 262 MET cc_start: 0.7502 (ttm) cc_final: 0.7215 (ttm) REVERT: B 317 CYS cc_start: 0.7258 (p) cc_final: 0.6754 (t) REVERT: B 335 PHE cc_start: 0.8329 (m-80) cc_final: 0.8077 (m-10) REVERT: C 13 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6733 (ttm110) REVERT: R 157 MET cc_start: 0.8118 (tmm) cc_final: 0.7554 (tmm) REVERT: R 170 MET cc_start: 0.6498 (mpp) cc_final: 0.5979 (pmm) REVERT: R 286 MET cc_start: 0.7271 (mmm) cc_final: 0.7026 (mmm) REVERT: S 21 SER cc_start: 0.7876 (t) cc_final: 0.7232 (p) REVERT: S 128 MET cc_start: 0.8141 (mmm) cc_final: 0.7479 (mmm) REVERT: S 212 VAL cc_start: 0.8934 (t) cc_final: 0.8536 (m) outliers start: 29 outliers final: 24 residues processed: 178 average time/residue: 0.2309 time to fit residues: 55.3224 Evaluate side-chains 176 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 218 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8977 Z= 0.275 Angle : 0.577 14.539 12168 Z= 0.289 Chirality : 0.043 0.172 1391 Planarity : 0.003 0.039 1525 Dihedral : 5.102 34.246 1229 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.49 % Allowed : 19.89 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.50 (0.24), residues: 1117 helix: 0.27 (0.26), residues: 393 sheet: -1.76 (0.30), residues: 246 loop : -1.55 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 47 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.002 PHE B 241 TYR 0.029 0.002 TYR S 178 ARG 0.004 0.000 ARG R 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6602 (m) cc_final: 0.6260 (t) REVERT: A 270 LYS cc_start: 0.7940 (mttt) cc_final: 0.7290 (mmtm) REVERT: A 304 GLN cc_start: 0.7752 (tt0) cc_final: 0.7289 (tt0) REVERT: A 306 GLN cc_start: 0.7249 (mt0) cc_final: 0.6802 (mt0) REVERT: B 59 TYR cc_start: 0.8481 (m-80) cc_final: 0.7894 (m-80) REVERT: B 188 MET cc_start: 0.7387 (mmm) cc_final: 0.6966 (mmm) REVERT: B 232 ILE cc_start: 0.8414 (tt) cc_final: 0.8004 (tt) REVERT: B 234 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: B 243 THR cc_start: 0.7945 (p) cc_final: 0.7588 (p) REVERT: B 262 MET cc_start: 0.7511 (ttm) cc_final: 0.7237 (ttm) REVERT: B 317 CYS cc_start: 0.7422 (p) cc_final: 0.6897 (t) REVERT: B 335 PHE cc_start: 0.8350 (m-80) cc_final: 0.8098 (m-10) REVERT: C 13 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6761 (ttm110) REVERT: R 42 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7252 (tp) REVERT: R 157 MET cc_start: 0.8274 (tmm) cc_final: 0.7545 (tmm) REVERT: R 170 MET cc_start: 0.6474 (mpp) cc_final: 0.5990 (pmm) REVERT: S 21 SER cc_start: 0.7831 (t) cc_final: 0.7201 (p) REVERT: S 128 MET cc_start: 0.8205 (mmm) cc_final: 0.7575 (mmm) REVERT: S 190 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7685 (ptt90) REVERT: S 212 VAL cc_start: 0.8968 (t) cc_final: 0.8573 (m) outliers start: 33 outliers final: 25 residues processed: 179 average time/residue: 0.2298 time to fit residues: 55.2116 Evaluate side-chains 179 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8977 Z= 0.220 Angle : 0.563 13.777 12168 Z= 0.279 Chirality : 0.042 0.184 1391 Planarity : 0.003 0.038 1525 Dihedral : 4.965 27.939 1229 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.17 % Allowed : 20.63 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.36 (0.24), residues: 1117 helix: 0.49 (0.26), residues: 394 sheet: -1.69 (0.29), residues: 255 loop : -1.56 (0.27), residues: 468 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 0.025 0.002 PHE A 189 TYR 0.028 0.001 TYR A 230 ARG 0.003 0.000 ARG R 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6702 (m) cc_final: 0.6315 (t) REVERT: A 270 LYS cc_start: 0.7918 (mttt) cc_final: 0.7278 (mmtm) REVERT: A 304 GLN cc_start: 0.7739 (tt0) cc_final: 0.7273 (tt0) REVERT: A 306 GLN cc_start: 0.7209 (mt0) cc_final: 0.6738 (mt0) REVERT: B 59 TYR cc_start: 0.8455 (m-80) cc_final: 0.8056 (m-80) REVERT: B 188 MET cc_start: 0.7459 (mmm) cc_final: 0.7064 (mmm) REVERT: B 232 ILE cc_start: 0.8439 (tt) cc_final: 0.8025 (tt) REVERT: B 234 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: B 243 THR cc_start: 0.7908 (p) cc_final: 0.7576 (p) REVERT: B 262 MET cc_start: 0.7513 (ttm) cc_final: 0.7235 (ttm) REVERT: B 317 CYS cc_start: 0.7261 (p) cc_final: 0.6790 (t) REVERT: B 335 PHE cc_start: 0.8348 (m-80) cc_final: 0.8104 (m-10) REVERT: C 13 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6765 (ttm110) REVERT: R 157 MET cc_start: 0.8257 (tmm) cc_final: 0.7503 (tmm) REVERT: S 128 MET cc_start: 0.8257 (mmm) cc_final: 0.7642 (mmm) REVERT: S 190 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7691 (ptt90) REVERT: S 212 VAL cc_start: 0.8955 (t) cc_final: 0.8554 (m) outliers start: 30 outliers final: 24 residues processed: 178 average time/residue: 0.2322 time to fit residues: 55.5859 Evaluate side-chains 177 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 190 ARG Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL 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: 1.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8977 Z= 0.172 Angle : 0.554 13.023 12168 Z= 0.272 Chirality : 0.042 0.281 1391 Planarity : 0.003 0.038 1525 Dihedral : 4.772 26.472 1229 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.75 % Allowed : 21.38 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.15 (0.25), residues: 1117 helix: 0.71 (0.27), residues: 394 sheet: -1.57 (0.30), residues: 256 loop : -1.49 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE S 27 TYR 0.029 0.001 TYR A 230 ARG 0.003 0.000 ARG R 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6564 (m) cc_final: 0.6175 (t) REVERT: A 270 LYS cc_start: 0.7976 (mttt) cc_final: 0.7389 (mmtm) REVERT: A 304 GLN cc_start: 0.7693 (tt0) cc_final: 0.7257 (tt0) REVERT: B 52 ARG cc_start: 0.8029 (mpt180) cc_final: 0.7793 (mpt180) REVERT: B 59 TYR cc_start: 0.8390 (m-80) cc_final: 0.7988 (m-80) REVERT: B 188 MET cc_start: 0.7520 (mmm) cc_final: 0.7121 (mmm) REVERT: B 215 GLU cc_start: 0.8251 (tp30) cc_final: 0.8044 (tp30) REVERT: B 234 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: B 243 THR cc_start: 0.7908 (p) cc_final: 0.7678 (p) REVERT: B 262 MET cc_start: 0.7531 (ttm) cc_final: 0.7258 (ttm) REVERT: B 317 CYS cc_start: 0.7200 (p) cc_final: 0.6742 (t) REVERT: B 335 PHE cc_start: 0.8336 (m-80) cc_final: 0.8107 (m-10) REVERT: C 13 ARG cc_start: 0.7038 (ttm110) cc_final: 0.6730 (ttm110) REVERT: R 157 MET cc_start: 0.8254 (tmm) cc_final: 0.7552 (tmm) REVERT: S 128 MET cc_start: 0.8238 (mmm) cc_final: 0.7606 (mmm) REVERT: S 212 VAL cc_start: 0.8850 (t) cc_final: 0.8435 (m) outliers start: 26 outliers final: 22 residues processed: 175 average time/residue: 0.2337 time to fit residues: 54.8876 Evaluate side-chains 172 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.0470 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 88 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8977 Z= 0.198 Angle : 0.565 13.232 12168 Z= 0.277 Chirality : 0.042 0.244 1391 Planarity : 0.003 0.037 1525 Dihedral : 4.682 26.470 1228 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.54 % Allowed : 21.90 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.06 (0.25), residues: 1117 helix: 0.83 (0.27), residues: 393 sheet: -1.55 (0.29), residues: 256 loop : -1.46 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS S 35 PHE 0.026 0.002 PHE A 189 TYR 0.029 0.001 TYR A 230 ARG 0.003 0.000 ARG R 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 THR cc_start: 0.6547 (m) cc_final: 0.6157 (t) REVERT: A 270 LYS cc_start: 0.7980 (mttt) cc_final: 0.7381 (mmtm) REVERT: A 304 GLN cc_start: 0.7672 (tt0) cc_final: 0.7237 (tt0) REVERT: A 306 GLN cc_start: 0.7201 (mt0) cc_final: 0.6653 (mt0) REVERT: B 52 ARG cc_start: 0.8033 (mpt180) cc_final: 0.7800 (mpt180) REVERT: B 59 TYR cc_start: 0.8424 (m-80) cc_final: 0.8089 (m-80) REVERT: B 188 MET cc_start: 0.7522 (mmm) cc_final: 0.7140 (mmm) REVERT: B 215 GLU cc_start: 0.8253 (tp30) cc_final: 0.8053 (tp30) REVERT: B 232 ILE cc_start: 0.8505 (tt) cc_final: 0.8183 (tt) REVERT: B 234 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: B 243 THR cc_start: 0.7990 (p) cc_final: 0.7772 (p) REVERT: B 262 MET cc_start: 0.7536 (ttm) cc_final: 0.7261 (ttm) REVERT: B 317 CYS cc_start: 0.7239 (p) cc_final: 0.6784 (t) REVERT: B 335 PHE cc_start: 0.8343 (m-80) cc_final: 0.8112 (m-10) REVERT: C 13 ARG cc_start: 0.7046 (ttm110) cc_final: 0.6740 (ttm110) REVERT: R 157 MET cc_start: 0.8260 (tmm) cc_final: 0.7614 (tmm) REVERT: S 128 MET cc_start: 0.8189 (mmm) cc_final: 0.7511 (mmm) outliers start: 24 outliers final: 21 residues processed: 168 average time/residue: 0.2457 time to fit residues: 54.7233 Evaluate side-chains 169 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 25 TYR Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.186143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146460 restraints weight = 9470.875| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.07 r_work: 0.3472 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8977 Z= 0.194 Angle : 0.565 12.814 12168 Z= 0.277 Chirality : 0.042 0.246 1391 Planarity : 0.003 0.037 1525 Dihedral : 4.648 26.480 1228 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.75 % Allowed : 21.90 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.99 (0.25), residues: 1117 helix: 0.91 (0.27), residues: 393 sheet: -1.55 (0.29), residues: 256 loop : -1.41 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE S 27 TYR 0.028 0.001 TYR A 230 ARG 0.003 0.000 ARG R 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.49 seconds wall clock time: 43 minutes 22.03 seconds (2602.03 seconds total)