Starting phenix.real_space_refine on Sat Feb 17 09:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwz_20928/02_2024/6uwz_20928_updated.pdb" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 108 5.16 5 C 11832 2.51 5 N 2857 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 331": "NH1" <-> "NH2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E ARG 6": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18330 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 bond proxies already assigned to first conformer: 3281 Chain: "B" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3462 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3204 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3337 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 546 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 64} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 546 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 64} Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'NAG': 2, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 11.78, per 1000 atoms: 0.64 Number of scatterers: 18330 At special positions: 0 Unit cell: (123.12, 165.24, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 5 15.00 O 3528 8.00 N 2857 7.00 C 11832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 44 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 33 " distance=2.04 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 59 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 23 " distance=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 44 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 33 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 59 " distance=2.02 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 65 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " " MAN H 5 " - " MAN H 6 " " MAN H 8 " - " MAN H 9 " " MAN K 4 " - " MAN K 5 " " MAN K 5 " - " MAN K 6 " " MAN K 8 " - " MAN K 9 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 7 " - " MAN H 10 " " BMA K 3 " - " MAN K 4 " " MAN K 7 " - " MAN K 10 " ALPHA1-6 " BMA H 3 " - " MAN H 7 " " MAN H 7 " - " MAN H 8 " " BMA K 3 " - " MAN K 7 " " MAN K 7 " - " MAN K 8 " " NAG L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " NAG-ASN " NAG B 604 " - " ASN B 70 " " NAG B 605 " - " ASN B 208 " " NAG E 506 " - " ASN E 68 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN B 143 " " NAG J 1 " - " ASN C 141 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.43 Conformation dependent library (CDL) restraints added in 3.9 seconds 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 25 sheets defined 36.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 69 through 72 Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 220 through 234 removed outlier: 4.653A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.725A pdb=" N GLU A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 320 through 322 No H-bonds generated for 'chain 'A' and resid 320 through 322' Processing helix chain 'A' and resid 371 through 424 removed outlier: 3.621A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.501A pdb=" N LEU B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.465A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 275 Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 417 through 477 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 218 through 239 Proline residue: C 227 - end of helix removed outlier: 5.287A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.225A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 220 through 229 Processing helix chain 'D' and resid 232 through 234 No H-bonds generated for 'chain 'D' and resid 232 through 234' Processing helix chain 'D' and resid 242 through 263 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 372 through 426 removed outlier: 3.703A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.857A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 removed outlier: 3.547A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'E' and resid 411 through 472 removed outlier: 3.842A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.912A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.465A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.383A pdb=" N VAL B 31 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP B 161 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE B 33 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= F, first strand: chain 'B' and resid 80 through 83 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.652A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= I, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.941A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.325A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 58 through 61 Processing sheet with id= L, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= M, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= N, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.780A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 156 through 160 removed outlier: 5.668A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.632A pdb=" N SER D 42 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.704A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 156 through 160 removed outlier: 6.484A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.570A pdb=" N SER E 42 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.294A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.943A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 2 through 5 removed outlier: 3.539A pdb=" N SER F 12 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.605A pdb=" N GLY F 43 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 2 through 5 removed outlier: 3.627A pdb=" N SER G 12 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 24 through 28 removed outlier: 3.556A pdb=" N TYR G 24 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY G 43 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP G 28 " --> pdb=" O VAL G 39 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 8.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2900 1.32 - 1.45: 5464 1.45 - 1.58: 10118 1.58 - 1.72: 10 1.72 - 1.85: 165 Bond restraints: 18657 Sorted by residual: bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV D 511 " pdb=" O31 POV D 511 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV C 705 " pdb=" O31 POV C 705 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C31 POV A 511 " pdb=" O31 POV A 511 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C21 POV A 511 " pdb=" O21 POV A 511 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 18652 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.78: 390 104.78 - 112.11: 9852 112.11 - 119.44: 5906 119.44 - 126.77: 8924 126.77 - 134.10: 351 Bond angle restraints: 25423 Sorted by residual: angle pdb=" O11 POV A 511 " pdb=" P POV A 511 " pdb=" O12 POV A 511 " ideal model delta sigma weight residual 97.67 110.21 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" O13 POV D 511 " pdb=" P POV D 511 " pdb=" O14 POV D 511 " ideal model delta sigma weight residual 121.11 109.00 12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O13 POV A 511 " pdb=" P POV A 511 " pdb=" O14 POV A 511 " ideal model delta sigma weight residual 121.11 109.04 12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O11 POV C 701 " pdb=" P POV C 701 " pdb=" O12 POV C 701 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV C 701 " pdb=" P POV C 701 " pdb=" O14 POV C 701 " ideal model delta sigma weight residual 121.11 109.36 11.75 3.00e+00 1.11e-01 1.53e+01 ... (remaining 25418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 11187 29.05 - 58.11: 353 58.11 - 87.16: 52 87.16 - 116.22: 18 116.22 - 145.27: 2 Dihedral angle restraints: 11612 sinusoidal: 5153 harmonic: 6459 Sorted by residual: dihedral pdb=" CB CYS F 29 " pdb=" SG CYS F 29 " pdb=" SG CYS F 33 " pdb=" CB CYS F 33 " ideal model delta sinusoidal sigma weight residual 93.00 25.37 67.63 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CB CYS G 60 " pdb=" SG CYS G 60 " pdb=" SG CYS G 65 " pdb=" CB CYS G 65 " ideal model delta sinusoidal sigma weight residual 93.00 28.78 64.22 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS F 48 " pdb=" SG CYS F 48 " pdb=" SG CYS F 59 " pdb=" CB CYS F 59 " ideal model delta sinusoidal sigma weight residual 93.00 149.30 -56.30 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 11609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2494 0.071 - 0.141: 512 0.141 - 0.212: 13 0.212 - 0.282: 3 0.282 - 0.353: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.37e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 chirality pdb=" C1 MAN H 6 " pdb=" O2 MAN H 5 " pdb=" C2 MAN H 6 " pdb=" O5 MAN H 6 " both_signs ideal model delta sigma weight residual False 2.40 2.19 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 3022 not shown) Planarity restraints: 3098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.138 2.00e-02 2.50e+03 1.13e-01 1.61e+02 pdb=" C7 NAG J 2 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.182 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.111 2.00e-02 2.50e+03 9.19e-02 1.06e+02 pdb=" C7 NAG I 2 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.147 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.087 2.00e-02 2.50e+03 7.14e-02 6.38e+01 pdb=" C7 NAG J 1 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.114 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.015 2.00e-02 2.50e+03 ... (remaining 3095 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 8 2.18 - 2.86: 6707 2.86 - 3.54: 25471 3.54 - 4.22: 47290 4.22 - 4.90: 81048 Nonbonded interactions: 160524 Sorted by model distance: nonbonded pdb=" OD2 ASP E 483 " pdb=" OH TYR E 487 " model vdw 1.501 2.440 nonbonded pdb=" O SER A 327 " pdb=" O13 POV A 511 " model vdw 2.020 3.040 nonbonded pdb=" OD2 ASP B 214 " pdb=" OG1 THR B 216 " model vdw 2.044 2.440 nonbonded pdb=" OE1 GLU B 280 " pdb=" OH TYR C 220 " model vdw 2.060 2.440 nonbonded pdb=" O VAL C 277 " pdb=" NH1 ARG C 282 " model vdw 2.074 2.520 ... (remaining 160519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 65 or resid 67 through 433 or resid 511)) selection = (chain 'D' and (resid 1 through 65 or resid 67 through 433 or (resid 511 and (na \ me N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C2 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C3 \ 8 or name C39 or name O11 or name O12 or name O13 or name O14 or name O21 or nam \ e O22 or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.020 Extract box with map and model: 12.500 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 54.280 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.011 0.095 18657 Z= 0.707 Angle : 0.821 12.537 25423 Z= 0.386 Chirality : 0.053 0.353 3025 Planarity : 0.006 0.113 3090 Dihedral : 15.212 145.270 7358 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % 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: -2.64 (0.16), residues: 2152 helix: -0.79 (0.16), residues: 792 sheet: -2.00 (0.21), residues: 461 loop : -2.40 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 60 HIS 0.005 0.001 HIS A 204 PHE 0.027 0.001 PHE A 284 TYR 0.013 0.002 TYR F 24 ARG 0.011 0.001 ARG D 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.105 Fit side-chains REVERT: A 330 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6857 (tttm) REVERT: A 415 MET cc_start: 0.7103 (mmt) cc_final: 0.6653 (mmp) REVERT: B 477 ASN cc_start: 0.6989 (t0) cc_final: 0.6698 (t160) REVERT: C 107 ASN cc_start: 0.7803 (p0) cc_final: 0.7295 (m-40) REVERT: C 244 ASP cc_start: 0.7200 (m-30) cc_final: 0.6697 (t0) REVERT: D 77 LYS cc_start: 0.8632 (mttm) cc_final: 0.8365 (mttt) REVERT: D 323 VAL cc_start: 0.8273 (t) cc_final: 0.7936 (t) REVERT: D 387 LYS cc_start: 0.7152 (ptpt) cc_final: 0.6779 (ptmm) REVERT: E 174 ASP cc_start: 0.7389 (t0) cc_final: 0.6491 (t0) REVERT: E 314 THR cc_start: 0.7669 (p) cc_final: 0.7399 (p) REVERT: E 471 HIS cc_start: 0.7412 (t-90) cc_final: 0.7172 (t-90) REVERT: G 26 LYS cc_start: 0.8405 (mtpt) cc_final: 0.7847 (mtmm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 1.3297 time to fit residues: 461.1740 Evaluate side-chains 229 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 168 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 95 ASN A 186 HIS A 204 HIS A 322 ASN A 394 ASN B 26 HIS B 95 GLN B 267 GLN C 140 GLN C 159 GLN C 310 ASN C 316 ASN C 320 GLN C 414 GLN D 58 GLN D 140 GLN D 208 GLN D 408 HIS E 27 HIS E 59 GLN E 140 GLN E 188 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18657 Z= 0.224 Angle : 0.593 8.268 25423 Z= 0.298 Chirality : 0.045 0.299 3025 Planarity : 0.005 0.047 3090 Dihedral : 10.489 109.964 3147 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 1.50 % Allowed : 10.37 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.78 (0.18), residues: 2152 helix: 1.07 (0.18), residues: 783 sheet: -1.41 (0.21), residues: 447 loop : -1.40 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 60 HIS 0.005 0.001 HIS F 4 PHE 0.011 0.001 PHE B 473 TYR 0.009 0.001 TYR C 210 ARG 0.009 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 242 time to evaluate : 2.144 Fit side-chains REVERT: A 330 LYS cc_start: 0.7267 (ttpt) cc_final: 0.7015 (tttm) REVERT: A 415 MET cc_start: 0.7328 (mmt) cc_final: 0.6865 (mmp) REVERT: B 186 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 477 ASN cc_start: 0.7106 (t0) cc_final: 0.6808 (t160) REVERT: C 50 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7760 (ttm) REVERT: C 107 ASN cc_start: 0.7913 (p0) cc_final: 0.7212 (m-40) REVERT: C 244 ASP cc_start: 0.7186 (m-30) cc_final: 0.6765 (t0) REVERT: E 471 HIS cc_start: 0.7389 (t-90) cc_final: 0.7118 (t-90) REVERT: F 55 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: G 26 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7455 (mtmm) outliers start: 30 outliers final: 10 residues processed: 252 average time/residue: 1.2567 time to fit residues: 357.3314 Evaluate side-chains 223 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS B 187 ASN C 111 GLN C 310 ASN C 316 ASN C 466 ASN D 186 HIS D 208 GLN E 250 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18657 Z= 0.344 Angle : 0.609 8.342 25423 Z= 0.307 Chirality : 0.046 0.242 3025 Planarity : 0.005 0.040 3090 Dihedral : 9.936 87.769 3147 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.29 % Allowed : 12.27 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2152 helix: 1.40 (0.19), residues: 791 sheet: -1.16 (0.22), residues: 452 loop : -1.12 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS D 204 PHE 0.015 0.002 PHE A 256 TYR 0.015 0.002 TYR D 381 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 2.060 Fit side-chains REVERT: A 415 MET cc_start: 0.7434 (mmt) cc_final: 0.6648 (mmp) REVERT: B 186 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: B 322 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8420 (tp) REVERT: B 441 GLU cc_start: 0.7659 (tp30) cc_final: 0.7378 (tm-30) REVERT: C 50 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: C 167 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.5882 (mp0) REVERT: C 214 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8053 (tp40) REVERT: C 244 ASP cc_start: 0.7285 (m-30) cc_final: 0.6936 (t0) REVERT: C 316 ASN cc_start: 0.7827 (m-40) cc_final: 0.7365 (m110) REVERT: C 410 TYR cc_start: 0.7717 (t80) cc_final: 0.7477 (t80) REVERT: E 471 HIS cc_start: 0.7455 (t-90) cc_final: 0.7151 (t-90) REVERT: G 26 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7622 (mtmm) outliers start: 46 outliers final: 14 residues processed: 255 average time/residue: 1.1544 time to fit residues: 334.8741 Evaluate side-chains 233 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 276 GLN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS C 111 GLN C 183 ASN C 310 ASN C 414 GLN C 466 ASN D 208 GLN E 271 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 18657 Z= 0.228 Angle : 0.552 8.783 25423 Z= 0.280 Chirality : 0.043 0.234 3025 Planarity : 0.004 0.062 3090 Dihedral : 9.215 81.675 3147 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 12.92 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.04 (0.18), residues: 2152 helix: 1.77 (0.19), residues: 779 sheet: -0.98 (0.22), residues: 449 loop : -0.92 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 28 HIS 0.004 0.001 HIS B 26 PHE 0.011 0.001 PHE D 256 TYR 0.009 0.001 TYR E 241 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.407 Fit side-chains revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7868 (ttp-110) REVERT: A 377 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: A 384 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7110 (tp30) REVERT: B 186 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: B 322 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8455 (tp) REVERT: B 441 GLU cc_start: 0.7683 (tp30) cc_final: 0.7375 (tm-30) REVERT: C 50 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: C 214 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8098 (tp40) REVERT: C 244 ASP cc_start: 0.7227 (m-30) cc_final: 0.6955 (t0) REVERT: C 316 ASN cc_start: 0.7821 (m-40) cc_final: 0.7373 (m110) REVERT: C 331 TRP cc_start: 0.7406 (m100) cc_final: 0.6865 (m-90) REVERT: D 108 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8733 (pp) REVERT: D 117 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7907 (tpp) REVERT: D 119 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8955 (m) REVERT: D 387 LYS cc_start: 0.7385 (ptmm) cc_final: 0.6798 (ptpt) REVERT: E 176 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: E 471 HIS cc_start: 0.7436 (t-90) cc_final: 0.7152 (t-90) outliers start: 55 outliers final: 20 residues processed: 260 average time/residue: 1.1480 time to fit residues: 340.4133 Evaluate side-chains 247 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 111 GLN C 310 ASN C 414 GLN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 18657 Z= 0.248 Angle : 0.550 10.350 25423 Z= 0.278 Chirality : 0.043 0.224 3025 Planarity : 0.004 0.066 3090 Dihedral : 9.037 78.451 3147 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 2.89 % Allowed : 14.06 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.21 (0.18), residues: 2152 helix: 1.91 (0.19), residues: 779 sheet: -0.82 (0.22), residues: 457 loop : -0.87 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.004 0.001 HIS B 26 PHE 0.011 0.001 PHE D 256 TYR 0.011 0.001 TYR C 410 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 227 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 207 MET cc_start: 0.8007 (ptp) cc_final: 0.7506 (ptt) REVERT: A 313 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7801 (ttp-110) REVERT: A 377 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: A 384 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7025 (tp30) REVERT: B 186 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: B 305 ASN cc_start: 0.7568 (OUTLIER) cc_final: 0.7104 (t0) REVERT: B 436 LYS cc_start: 0.7441 (tttm) cc_final: 0.7064 (ttpt) REVERT: B 441 GLU cc_start: 0.7747 (tp30) cc_final: 0.7404 (tm-30) REVERT: C 50 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7984 (ttm) REVERT: C 214 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8063 (tp40) REVERT: C 244 ASP cc_start: 0.7252 (m-30) cc_final: 0.6965 (t0) REVERT: C 316 ASN cc_start: 0.7815 (m-40) cc_final: 0.7364 (m110) REVERT: C 331 TRP cc_start: 0.7393 (m100) cc_final: 0.6869 (m-90) REVERT: D 108 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8732 (pp) REVERT: D 119 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8946 (m) REVERT: D 164 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8059 (mtm180) REVERT: D 387 LYS cc_start: 0.7392 (ptmm) cc_final: 0.6812 (ptpt) REVERT: E 176 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: E 471 HIS cc_start: 0.7456 (t-90) cc_final: 0.7162 (t-90) outliers start: 58 outliers final: 26 residues processed: 259 average time/residue: 1.1171 time to fit residues: 330.9660 Evaluate side-chains 255 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN C 111 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 466 ASN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.154 18657 Z= 0.208 Angle : 0.529 10.209 25423 Z= 0.266 Chirality : 0.043 0.237 3025 Planarity : 0.004 0.065 3090 Dihedral : 8.724 77.571 3147 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.54 % Allowed : 14.91 % Favored : 82.54 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 2152 helix: 2.09 (0.19), residues: 777 sheet: -0.74 (0.23), residues: 458 loop : -0.74 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.005 0.001 HIS B 26 PHE 0.010 0.001 PHE E 467 TYR 0.010 0.001 TYR C 410 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8285 (p0) REVERT: A 313 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7953 (ttm-80) REVERT: A 377 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 415 MET cc_start: 0.7464 (mmt) cc_final: 0.7207 (mmp) REVERT: B 186 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: B 283 LEU cc_start: 0.8603 (mt) cc_final: 0.8359 (mm) REVERT: B 436 LYS cc_start: 0.7461 (tttm) cc_final: 0.7083 (ttpt) REVERT: B 441 GLU cc_start: 0.7748 (tp30) cc_final: 0.7416 (tm-30) REVERT: C 50 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7941 (ttm) REVERT: C 214 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8087 (tp40) REVERT: C 244 ASP cc_start: 0.7240 (m-30) cc_final: 0.6972 (t0) REVERT: C 316 ASN cc_start: 0.7778 (m-40) cc_final: 0.7350 (m110) REVERT: C 331 TRP cc_start: 0.7352 (m100) cc_final: 0.6890 (m-90) REVERT: D 108 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (pp) REVERT: D 111 ASP cc_start: 0.7742 (m-30) cc_final: 0.7516 (m-30) REVERT: D 117 MET cc_start: 0.8404 (tpp) cc_final: 0.7989 (tpp) REVERT: D 164 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7875 (mtm180) REVERT: D 262 GLU cc_start: 0.6150 (tt0) cc_final: 0.5500 (tp30) REVERT: D 387 LYS cc_start: 0.7403 (ptmm) cc_final: 0.6555 (pttp) REVERT: E 101 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: E 176 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6366 (pm20) REVERT: E 471 HIS cc_start: 0.7426 (t-90) cc_final: 0.7132 (t-90) outliers start: 51 outliers final: 21 residues processed: 259 average time/residue: 1.1342 time to fit residues: 334.4664 Evaluate side-chains 248 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.4980 chunk 116 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 305 ASN C 111 GLN C 310 ASN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 18657 Z= 0.191 Angle : 0.524 10.167 25423 Z= 0.261 Chirality : 0.042 0.239 3025 Planarity : 0.004 0.094 3090 Dihedral : 8.533 77.946 3147 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 2.49 % Allowed : 15.76 % Favored : 81.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.53 (0.18), residues: 2152 helix: 2.24 (0.19), residues: 769 sheet: -0.67 (0.23), residues: 454 loop : -0.70 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 118 HIS 0.005 0.001 HIS B 26 PHE 0.011 0.001 PHE E 467 TYR 0.015 0.001 TYR C 410 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8278 (p0) REVERT: A 313 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7970 (ttm-80) REVERT: A 377 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 380 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7903 (mtmm) REVERT: B 186 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: B 283 LEU cc_start: 0.8616 (mt) cc_final: 0.8410 (mm) REVERT: B 436 LYS cc_start: 0.7458 (tttm) cc_final: 0.7073 (ttpt) REVERT: B 441 GLU cc_start: 0.7747 (tp30) cc_final: 0.7417 (tm-30) REVERT: C 50 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7935 (ttm) REVERT: C 107 ASN cc_start: 0.7900 (p0) cc_final: 0.7062 (m-40) REVERT: C 214 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8060 (tp40) REVERT: C 244 ASP cc_start: 0.7250 (m-30) cc_final: 0.6987 (t0) REVERT: C 316 ASN cc_start: 0.7814 (m-40) cc_final: 0.7387 (m110) REVERT: C 331 TRP cc_start: 0.7342 (m100) cc_final: 0.6912 (m-90) REVERT: D 108 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8704 (pp) REVERT: D 117 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7946 (tpp) REVERT: D 164 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7884 (mtm180) REVERT: D 262 GLU cc_start: 0.6219 (tt0) cc_final: 0.5549 (tp30) REVERT: D 264 ILE cc_start: 0.7358 (pt) cc_final: 0.6996 (mp) REVERT: D 387 LYS cc_start: 0.7421 (ptmm) cc_final: 0.6617 (pttp) REVERT: E 101 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: E 471 HIS cc_start: 0.7432 (t-90) cc_final: 0.7155 (t-90) REVERT: G 41 GLU cc_start: 0.7606 (tt0) cc_final: 0.7064 (tt0) outliers start: 50 outliers final: 18 residues processed: 265 average time/residue: 1.1569 time to fit residues: 350.9099 Evaluate side-chains 250 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 162 optimal weight: 0.0670 chunk 188 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 305 ASN C 53 ASN C 111 GLN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 18657 Z= 0.226 Angle : 0.541 10.139 25423 Z= 0.270 Chirality : 0.043 0.239 3025 Planarity : 0.004 0.087 3090 Dihedral : 8.605 81.895 3147 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.95 % Allowed : 16.81 % Favored : 81.25 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2152 helix: 2.24 (0.19), residues: 768 sheet: -0.66 (0.23), residues: 457 loop : -0.69 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 28 HIS 0.005 0.001 HIS B 26 PHE 0.014 0.001 PHE E 478 TYR 0.017 0.001 TYR D 381 ARG 0.007 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: A 380 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7909 (mtmm) REVERT: B 186 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: B 283 LEU cc_start: 0.8621 (mt) cc_final: 0.8410 (mm) REVERT: B 436 LYS cc_start: 0.7467 (tttm) cc_final: 0.7109 (ttpt) REVERT: B 441 GLU cc_start: 0.7782 (tp30) cc_final: 0.7439 (tm-30) REVERT: C 50 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7980 (ttm) REVERT: C 214 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8019 (tp40) REVERT: C 244 ASP cc_start: 0.7251 (m-30) cc_final: 0.6995 (t0) REVERT: C 316 ASN cc_start: 0.7783 (m-40) cc_final: 0.7244 (m110) REVERT: C 331 TRP cc_start: 0.7350 (m100) cc_final: 0.6919 (m-90) REVERT: D 108 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8740 (pp) REVERT: D 117 MET cc_start: 0.8391 (tpp) cc_final: 0.7971 (tpp) REVERT: D 164 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7870 (mtm180) REVERT: D 262 GLU cc_start: 0.6210 (tt0) cc_final: 0.5537 (tp30) REVERT: D 264 ILE cc_start: 0.7375 (pt) cc_final: 0.6963 (mp) REVERT: D 387 LYS cc_start: 0.7436 (ptmm) cc_final: 0.6637 (pttp) REVERT: E 101 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: E 176 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: E 471 HIS cc_start: 0.7445 (t-90) cc_final: 0.7145 (t-90) outliers start: 39 outliers final: 19 residues processed: 246 average time/residue: 1.1778 time to fit residues: 330.4889 Evaluate side-chains 243 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 59 optimal weight: 0.0000 chunk 174 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 0.0370 chunk 126 optimal weight: 4.9990 overall best weight: 0.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 ASN B 213 GLN B 305 ASN C 111 GLN C 320 GLN C 466 ASN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 18657 Z= 0.175 Angle : 0.516 9.947 25423 Z= 0.257 Chirality : 0.042 0.247 3025 Planarity : 0.004 0.097 3090 Dihedral : 8.319 82.406 3147 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 1.65 % Allowed : 17.01 % Favored : 81.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.64 (0.19), residues: 2152 helix: 2.37 (0.19), residues: 768 sheet: -0.62 (0.23), residues: 478 loop : -0.66 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS B 26 PHE 0.012 0.001 PHE E 467 TYR 0.016 0.001 TYR C 410 ARG 0.005 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7975 (ttp-110) REVERT: A 377 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: A 380 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7900 (mtmm) REVERT: B 436 LYS cc_start: 0.7448 (tttm) cc_final: 0.7082 (ttpt) REVERT: B 441 GLU cc_start: 0.7742 (tp30) cc_final: 0.7418 (tm-30) REVERT: C 50 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7877 (ttm) REVERT: C 107 ASN cc_start: 0.7807 (p0) cc_final: 0.7123 (m-40) REVERT: C 214 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8063 (tp40) REVERT: C 244 ASP cc_start: 0.7202 (m-30) cc_final: 0.6959 (t0) REVERT: C 316 ASN cc_start: 0.7661 (m-40) cc_final: 0.7244 (m110) REVERT: C 331 TRP cc_start: 0.7326 (m100) cc_final: 0.6923 (m-90) REVERT: D 117 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7981 (tpp) REVERT: D 164 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: D 262 GLU cc_start: 0.6210 (tt0) cc_final: 0.5544 (tp30) REVERT: D 264 ILE cc_start: 0.7329 (pt) cc_final: 0.6973 (mp) REVERT: D 387 LYS cc_start: 0.7407 (ptmm) cc_final: 0.7181 (ttmt) REVERT: D 416 LEU cc_start: 0.7938 (tp) cc_final: 0.7107 (mm) REVERT: E 101 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7207 (mm-30) REVERT: E 471 HIS cc_start: 0.7443 (t-90) cc_final: 0.7150 (t-90) REVERT: G 41 GLU cc_start: 0.7659 (tt0) cc_final: 0.7271 (tt0) outliers start: 33 outliers final: 19 residues processed: 243 average time/residue: 1.1697 time to fit residues: 323.3378 Evaluate side-chains 242 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 170 optimal weight: 0.0570 chunk 17 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 305 ASN C 53 ASN C 111 GLN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 18657 Z= 0.231 Angle : 0.547 10.609 25423 Z= 0.272 Chirality : 0.043 0.243 3025 Planarity : 0.004 0.095 3090 Dihedral : 8.530 84.579 3147 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 1.55 % Allowed : 17.56 % Favored : 80.90 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.63 (0.19), residues: 2152 helix: 2.32 (0.19), residues: 768 sheet: -0.62 (0.23), residues: 457 loop : -0.62 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 187 HIS 0.005 0.001 HIS B 26 PHE 0.014 0.001 PHE E 478 TYR 0.016 0.001 TYR C 410 ARG 0.006 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8004 (ttp-110) REVERT: A 377 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: A 380 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7905 (mtmm) REVERT: B 186 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: B 436 LYS cc_start: 0.7469 (tttm) cc_final: 0.7097 (ttpt) REVERT: B 441 GLU cc_start: 0.7796 (tp30) cc_final: 0.7454 (tm-30) REVERT: C 50 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7964 (ttm) REVERT: C 214 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8018 (tp40) REVERT: C 244 ASP cc_start: 0.7247 (m-30) cc_final: 0.6978 (t0) REVERT: C 316 ASN cc_start: 0.7664 (m-40) cc_final: 0.7220 (m110) REVERT: C 331 TRP cc_start: 0.7326 (m100) cc_final: 0.6930 (m-90) REVERT: C 415 LEU cc_start: 0.7931 (mp) cc_final: 0.7619 (mt) REVERT: D 117 MET cc_start: 0.8386 (tpp) cc_final: 0.7968 (tpp) REVERT: D 164 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7862 (mtm180) REVERT: D 264 ILE cc_start: 0.7365 (pt) cc_final: 0.6961 (mp) REVERT: D 387 LYS cc_start: 0.7422 (ptmm) cc_final: 0.7165 (ttmt) REVERT: E 101 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: E 471 HIS cc_start: 0.7442 (t-90) cc_final: 0.7142 (t-90) REVERT: G 41 GLU cc_start: 0.7686 (tt0) cc_final: 0.7271 (tt0) outliers start: 31 outliers final: 19 residues processed: 233 average time/residue: 1.1908 time to fit residues: 316.1340 Evaluate side-chains 239 residues out of total 2003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 214 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 164 ARG Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 52 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 305 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN D 208 GLN ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107636 restraints weight = 30154.228| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.91 r_work: 0.3034 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 18657 Z= 0.232 Angle : 0.548 10.058 25423 Z= 0.272 Chirality : 0.043 0.243 3025 Planarity : 0.004 0.093 3090 Dihedral : 8.561 86.106 3147 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.65 % Allowed : 17.51 % Favored : 80.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2152 helix: 2.22 (0.19), residues: 780 sheet: -0.62 (0.23), residues: 457 loop : -0.69 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 187 HIS 0.006 0.001 HIS B 26 PHE 0.011 0.001 PHE D 256 TYR 0.015 0.001 TYR C 410 ARG 0.006 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6500.72 seconds wall clock time: 116 minutes 59.29 seconds (7019.29 seconds total)