Starting phenix.real_space_refine on Fri Feb 16 01:42:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq5_30436/02_2024/7cq5_30436_updated.pdb" } resolution = 2.6 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 92 5.16 5 Cl 4 4.86 5 C 9007 2.51 5 N 2328 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13942 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5289 Classifications: {'peptide': 681} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 5264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5264 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 650} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CL': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CL': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.39, per 1000 atoms: 0.53 Number of scatterers: 13942 At special positions: 0 Unit cell: (134.23, 114.745, 136.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 92 16.00 P 6 15.00 O 2505 8.00 N 2328 7.00 C 9007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.02 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.04 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " 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=3, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.6 seconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 7 sheets defined 58.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 82 through 104 removed outlier: 4.152A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 116 through 127 removed outlier: 3.618A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 225 through 244 Processing helix chain 'A' and resid 256 through 270 removed outlier: 3.890A pdb=" N ALA A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.908A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 104 removed outlier: 3.585A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 116 through 127 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 174 No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.637A pdb=" N ASN B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.589A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.634A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 305 removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 122 through 169 removed outlier: 3.579A pdb=" N ARG C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 195 removed outlier: 3.660A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.553A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 261 removed outlier: 3.584A pdb=" N ILE C 251 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 254 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 283 through 301 removed outlier: 3.526A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 Processing helix chain 'C' and resid 321 through 345 Processing helix chain 'C' and resid 375 through 405 removed outlier: 3.788A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 433 removed outlier: 3.603A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 487 through 504 removed outlier: 3.781A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 535 Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.515A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 Processing helix chain 'C' and resid 578 through 596 removed outlier: 3.545A pdb=" N PHE C 581 " --> pdb=" O THR C 578 " (cutoff:3.500A) Proline residue: C 582 - end of helix removed outlier: 3.511A pdb=" N ALA C 590 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP C 595 " --> pdb=" O ILE C 592 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 596 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 4.184A pdb=" N GLN C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 629 No H-bonds generated for 'chain 'C' and resid 627 through 629' Processing helix chain 'C' and resid 644 through 651 Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 721 through 723 No H-bonds generated for 'chain 'C' and resid 721 through 723' Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 754 through 764 removed outlier: 3.618A pdb=" N LEU C 760 " --> pdb=" O ARG C 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 Processing helix chain 'D' and resid 122 through 169 removed outlier: 3.746A pdb=" N ARG D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 195 removed outlier: 3.574A pdb=" N TRP D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 206 through 214 Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.634A pdb=" N HIS D 252 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER D 253 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 254 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE D 261 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 301 Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 321 through 345 Processing helix chain 'D' and resid 372 through 405 Proline residue: D 376 - end of helix removed outlier: 3.535A pdb=" N GLY D 385 " --> pdb=" O GLY D 382 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 388 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY D 389 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 395 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP D 398 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET D 401 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 402 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 433 removed outlier: 3.503A pdb=" N ILE D 415 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'D' and resid 487 through 503 removed outlier: 3.718A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 535 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 544 through 559 removed outlier: 3.908A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.556A pdb=" N VAL D 568 " --> pdb=" O LEU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 595 removed outlier: 3.747A pdb=" N PHE D 581 " --> pdb=" O THR D 578 " (cutoff:3.500A) Proline residue: D 582 - end of helix removed outlier: 3.512A pdb=" N ALA D 590 " --> pdb=" O LEU D 587 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 593 " --> pdb=" O ALA D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.514A pdb=" N HIS D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 622 No H-bonds generated for 'chain 'D' and resid 620 through 622' Processing helix chain 'D' and resid 644 through 650 removed outlier: 3.728A pdb=" N ASP D 649 " --> pdb=" O GLY D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 689 removed outlier: 3.654A pdb=" N LEU D 688 " --> pdb=" O LEU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 723 No H-bonds generated for 'chain 'D' and resid 721 through 723' Processing helix chain 'D' and resid 729 through 731 No H-bonds generated for 'chain 'D' and resid 729 through 731' Processing helix chain 'D' and resid 754 through 762 removed outlier: 3.503A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 760 " --> pdb=" O ARG D 756 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 761 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 788 No H-bonds generated for 'chain 'D' and resid 785 through 788' Processing sheet with id= A, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= B, first strand: chain 'C' and resid 641 through 643 removed outlier: 4.078A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 747 through 749 removed outlier: 6.314A pdb=" N VAL C 770 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 660 through 664 Processing sheet with id= E, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.551A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 660 through 663 Processing sheet with id= G, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.539A pdb=" N VAL D 770 " --> pdb=" O VAL D 748 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 675 hydrogen bonds defined for protein. 1863 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: 4.11 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3794 1.33 - 1.46: 3367 1.46 - 1.58: 6942 1.58 - 1.71: 10 1.71 - 1.83: 140 Bond restraints: 14253 Sorted by residual: bond pdb=" CG1 ILE C 206 " pdb=" CD1 ILE C 206 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.33e+00 bond pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " ideal model delta sigma weight residual 1.532 1.562 -0.030 1.48e-02 4.57e+03 4.06e+00 bond pdb=" O5' ATP D 901 " pdb=" PA ATP D 901 " ideal model delta sigma weight residual 1.579 1.601 -0.022 1.10e-02 8.26e+03 4.03e+00 bond pdb=" C LEU B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.01e+00 bond pdb=" O2B ATP C 901 " pdb=" PB ATP C 901 " ideal model delta sigma weight residual 1.529 1.485 0.044 2.20e-02 2.07e+03 3.92e+00 ... (remaining 14248 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.76: 314 105.76 - 112.89: 7481 112.89 - 120.01: 5429 120.01 - 127.13: 5966 127.13 - 134.26: 184 Bond angle restraints: 19374 Sorted by residual: angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 133.22 6.65 1.00e+00 1.00e+00 4.42e+01 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 134.19 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 131.25 5.58 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C LEU C 97 " pdb=" N ASP C 98 " pdb=" CA ASP C 98 " ideal model delta sigma weight residual 122.63 130.28 -7.65 1.44e+00 4.82e-01 2.82e+01 ... (remaining 19369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 8029 16.18 - 32.36: 393 32.36 - 48.54: 88 48.54 - 64.71: 21 64.71 - 80.89: 9 Dihedral angle restraints: 8540 sinusoidal: 3399 harmonic: 5141 Sorted by residual: dihedral pdb=" CA ASP A 90 " pdb=" C ASP A 90 " pdb=" N PHE A 91 " pdb=" CA PHE A 91 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA CYS A 115 " pdb=" C CYS A 115 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA SER D 447 " pdb=" C SER D 447 " pdb=" N TYR D 448 " pdb=" CA TYR D 448 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1796 0.067 - 0.133: 401 0.133 - 0.199: 52 0.199 - 0.266: 12 0.266 - 0.332: 4 Chirality restraints: 2265 Sorted by residual: chirality pdb=" CG LEU D 687 " pdb=" CB LEU D 687 " pdb=" CD1 LEU D 687 " pdb=" CD2 LEU D 687 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CG LEU A 89 " pdb=" CB LEU A 89 " pdb=" CD1 LEU A 89 " pdb=" CD2 LEU A 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ASP C 98 " pdb=" N ASP C 98 " pdb=" C ASP C 98 " pdb=" CB ASP C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2262 not shown) Planarity restraints: 2422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.030 2.00e-02 2.50e+03 2.49e-02 1.56e+01 pdb=" CG TRP C 179 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 179 " 0.031 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP D 179 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 179 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 179 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 179 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 503 " -0.022 2.00e-02 2.50e+03 1.76e-02 7.75e+00 pdb=" CG TRP C 503 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP C 503 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 503 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 503 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 503 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 503 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 503 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 503 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 503 " 0.002 2.00e-02 2.50e+03 ... (remaining 2419 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 748 2.73 - 3.27: 13851 3.27 - 3.81: 22911 3.81 - 4.36: 28481 4.36 - 4.90: 48057 Nonbonded interactions: 114048 Sorted by model distance: nonbonded pdb=" OG SER D 298 " pdb=" OG1 THR D 335 " model vdw 2.185 2.440 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.246 2.440 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.263 2.440 nonbonded pdb=" O LEU C 500 " pdb=" OG1 THR C 504 " model vdw 2.280 2.440 nonbonded pdb=" O ILE D 163 " pdb=" OG1 THR D 167 " model vdw 2.286 2.440 ... (remaining 114043 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 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 652 or (resid 653 through 656 and (name N or na \ me CA or name C or name O or name CB )) or resid 657 through 664 or resid 673 th \ rough 694 or resid 706 through 789 or (resid 790 and (name N or name CA or name \ C or name O or name CB )) or resid 901 through 903)) selection = (chain 'D' and (resid 94 through 366 or (resid 367 and (name N or name CA or nam \ e C or name O or name CB )) or resid 368 through 619 or (resid 620 and (name N o \ r name CA or name C or name O or name CB )) or resid 621 through 694 or resid 70 \ 6 through 790 or resid 901 through 903)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.580 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.090 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.007 0.081 14253 Z= 0.452 Angle : 1.051 17.538 19374 Z= 0.574 Chirality : 0.059 0.332 2265 Planarity : 0.008 0.067 2420 Dihedral : 10.935 80.892 5176 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.46 % Allowed : 2.98 % Favored : 96.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 1746 helix: -2.22 (0.11), residues: 1107 sheet: -3.08 (1.18), residues: 5 loop : -2.89 (0.21), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP C 179 HIS 0.015 0.002 HIS D 479 PHE 0.038 0.004 PHE D 288 TYR 0.026 0.003 TYR A 188 ARG 0.020 0.002 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 1.741 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6965 (tm-30) REVERT: A 198 THR cc_start: 0.7701 (p) cc_final: 0.7496 (t) REVERT: B 222 LYS cc_start: 0.6868 (tmtp) cc_final: 0.6652 (mtpt) REVERT: B 260 ASP cc_start: 0.8093 (t70) cc_final: 0.7746 (t70) REVERT: C 271 ARG cc_start: 0.6363 (mmt90) cc_final: 0.6138 (ttp-170) REVERT: C 617 GLU cc_start: 0.7248 (pt0) cc_final: 0.6872 (pm20) REVERT: C 717 ARG cc_start: 0.6694 (mpt180) cc_final: 0.5634 (mmt180) REVERT: D 691 LYS cc_start: 0.8609 (mttm) cc_final: 0.8389 (mtmt) REVERT: D 728 GLN cc_start: 0.7985 (tp40) cc_final: 0.7630 (tp40) outliers start: 7 outliers final: 4 residues processed: 282 average time/residue: 1.6100 time to fit residues: 489.4600 Evaluate side-chains 166 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 162 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 611 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B 170 ASN C 115 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 348 ASN C 555 GLN ** C 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS D 263 GLN ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 555 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14253 Z= 0.178 Angle : 0.621 10.050 19374 Z= 0.321 Chirality : 0.041 0.181 2265 Planarity : 0.005 0.047 2420 Dihedral : 8.352 84.268 2061 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.78 % Allowed : 9.13 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1746 helix: -0.06 (0.15), residues: 1106 sheet: -2.77 (1.04), residues: 5 loop : -2.37 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 179 HIS 0.005 0.001 HIS C 658 PHE 0.019 0.002 PHE C 329 TYR 0.013 0.001 TYR C 715 ARG 0.005 0.001 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 1.721 Fit side-chains REVERT: B 148 MET cc_start: 0.6987 (mpp) cc_final: 0.6637 (mpp) REVERT: B 260 ASP cc_start: 0.8113 (t70) cc_final: 0.7801 (t70) REVERT: B 281 ASP cc_start: 0.7201 (t0) cc_final: 0.6954 (t0) REVERT: C 110 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: C 123 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: C 514 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: C 617 GLU cc_start: 0.7256 (pt0) cc_final: 0.6856 (pm20) REVERT: C 631 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7058 (pp-130) REVERT: C 641 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6828 (mtt90) REVERT: C 717 ARG cc_start: 0.6571 (mpt180) cc_final: 0.5555 (mmt180) REVERT: C 775 ARG cc_start: 0.6972 (mpp80) cc_final: 0.6655 (mpp-170) REVERT: C 778 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8567 (t) REVERT: D 349 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6413 (tmt) REVERT: D 691 LYS cc_start: 0.8548 (mttm) cc_final: 0.8291 (mtmt) REVERT: D 728 GLN cc_start: 0.7973 (tp40) cc_final: 0.7538 (tp40) outliers start: 42 outliers final: 14 residues processed: 201 average time/residue: 1.5556 time to fit residues: 338.2077 Evaluate side-chains 163 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 113 GLN B 242 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 777 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14253 Z= 0.171 Angle : 0.591 9.172 19374 Z= 0.302 Chirality : 0.040 0.194 2265 Planarity : 0.004 0.046 2420 Dihedral : 7.768 81.112 2058 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.58 % Allowed : 10.99 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1746 helix: 0.74 (0.16), residues: 1111 sheet: -2.51 (1.46), residues: 5 loop : -2.17 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 PHE 0.016 0.001 PHE C 329 TYR 0.014 0.001 TYR A 116 ARG 0.004 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6693 (tm-30) REVERT: B 104 ARG cc_start: 0.8254 (mtt90) cc_final: 0.7932 (mtt-85) REVERT: B 110 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7664 (mpt-90) REVERT: B 148 MET cc_start: 0.7089 (mpp) cc_final: 0.6792 (mpp) REVERT: B 152 MET cc_start: 0.7502 (ttm) cc_final: 0.7227 (ttt) REVERT: C 110 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7861 (tp30) REVERT: C 123 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: C 617 GLU cc_start: 0.7282 (pt0) cc_final: 0.6831 (pm20) REVERT: C 631 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7226 (pp-130) REVERT: C 717 ARG cc_start: 0.6619 (mpt180) cc_final: 0.5467 (mmt180) REVERT: C 775 ARG cc_start: 0.6960 (mpp80) cc_final: 0.6695 (mpp-170) REVERT: C 778 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8512 (t) REVERT: C 786 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7786 (p0) REVERT: D 728 GLN cc_start: 0.7979 (tp40) cc_final: 0.7552 (tp40) REVERT: D 775 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7080 (ttp80) REVERT: D 777 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6961 (mp10) outliers start: 39 outliers final: 21 residues processed: 180 average time/residue: 1.5910 time to fit residues: 308.8497 Evaluate side-chains 165 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 777 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN B 223 ASN ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 776 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14253 Z= 0.161 Angle : 0.550 8.284 19374 Z= 0.282 Chirality : 0.039 0.152 2265 Planarity : 0.004 0.045 2420 Dihedral : 7.279 78.549 2058 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.11 % Allowed : 11.52 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1746 helix: 1.28 (0.16), residues: 1104 sheet: -1.94 (1.74), residues: 5 loop : -2.05 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 PHE 0.015 0.001 PHE C 329 TYR 0.013 0.001 TYR C 715 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.655 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5250 (tm-30) REVERT: A 160 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 168 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: B 110 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7613 (mpt-90) REVERT: B 148 MET cc_start: 0.7091 (mpp) cc_final: 0.6728 (mpp) REVERT: B 281 ASP cc_start: 0.7228 (t0) cc_final: 0.6958 (t0) REVERT: C 123 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: C 514 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: C 617 GLU cc_start: 0.7269 (pt0) cc_final: 0.6819 (pm20) REVERT: C 631 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7335 (pp-130) REVERT: C 717 ARG cc_start: 0.6652 (mpt180) cc_final: 0.5288 (mmt180) REVERT: D 641 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7769 (mtm180) REVERT: D 728 GLN cc_start: 0.8025 (tp40) cc_final: 0.7582 (tp40) outliers start: 47 outliers final: 19 residues processed: 184 average time/residue: 1.5823 time to fit residues: 315.1748 Evaluate side-chains 171 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 641 ARG Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 757 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 42 optimal weight: 0.0060 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14253 Z= 0.187 Angle : 0.565 8.572 19374 Z= 0.290 Chirality : 0.041 0.165 2265 Planarity : 0.004 0.048 2420 Dihedral : 7.233 79.344 2056 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.91 % Allowed : 12.11 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1746 helix: 1.45 (0.16), residues: 1106 sheet: -1.80 (1.91), residues: 5 loop : -1.99 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 524 HIS 0.005 0.001 HIS C 220 PHE 0.016 0.001 PHE C 329 TYR 0.015 0.001 TYR C 715 ARG 0.005 0.001 ARG C 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.6170 (pm20) cc_final: 0.5351 (tm-30) REVERT: B 110 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7658 (mpt-90) REVERT: B 148 MET cc_start: 0.7104 (mpp) cc_final: 0.6747 (mpp) REVERT: B 152 MET cc_start: 0.7314 (ttt) cc_final: 0.7088 (mmm) REVERT: B 281 ASP cc_start: 0.7262 (t0) cc_final: 0.6943 (t0) REVERT: C 123 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: C 514 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: C 617 GLU cc_start: 0.7333 (pt0) cc_final: 0.6948 (pm20) REVERT: C 631 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7414 (pp-130) REVERT: C 717 ARG cc_start: 0.6818 (mpt180) cc_final: 0.5382 (mmt180) REVERT: D 97 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7270 (mt) REVERT: D 269 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7795 (mt) REVERT: D 332 MET cc_start: 0.8417 (mmm) cc_final: 0.7988 (mmm) REVERT: D 349 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6383 (tmt) REVERT: D 628 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7737 (ttm170) REVERT: D 641 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7793 (mtm180) REVERT: D 728 GLN cc_start: 0.8060 (tp40) cc_final: 0.7633 (tp40) REVERT: D 777 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: D 781 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8452 (mt) outliers start: 44 outliers final: 26 residues processed: 180 average time/residue: 1.6227 time to fit residues: 314.9244 Evaluate side-chains 177 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 641 ARG Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 777 GLN Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 0.0570 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14253 Z= 0.171 Angle : 0.550 8.176 19374 Z= 0.282 Chirality : 0.040 0.152 2265 Planarity : 0.004 0.047 2420 Dihedral : 7.080 78.698 2056 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.18 % Allowed : 12.31 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1746 helix: 1.61 (0.16), residues: 1099 sheet: -1.76 (1.93), residues: 5 loop : -1.95 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 PHE 0.016 0.001 PHE C 329 TYR 0.013 0.001 TYR D 505 ARG 0.006 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 86 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5332 (tm-30) REVERT: A 167 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6857 (mp10) REVERT: B 110 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7656 (mpt-90) REVERT: B 148 MET cc_start: 0.7124 (mpp) cc_final: 0.6749 (mpp) REVERT: B 281 ASP cc_start: 0.7264 (t0) cc_final: 0.6934 (t0) REVERT: C 401 MET cc_start: 0.8314 (mmm) cc_final: 0.8105 (mmp) REVERT: C 514 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: C 617 GLU cc_start: 0.7375 (pt0) cc_final: 0.7000 (pm20) REVERT: C 631 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7447 (pp-130) REVERT: C 717 ARG cc_start: 0.6880 (mpt180) cc_final: 0.5394 (mmt180) REVERT: D 97 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7287 (mt) REVERT: D 269 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7800 (mt) REVERT: D 332 MET cc_start: 0.8436 (mmm) cc_final: 0.8126 (mmm) REVERT: D 349 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6371 (tmm) REVERT: D 584 MET cc_start: 0.8518 (ttp) cc_final: 0.8293 (ttp) REVERT: D 588 MET cc_start: 0.8241 (mtp) cc_final: 0.7997 (mtm) REVERT: D 628 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7734 (ttm170) REVERT: D 641 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7761 (mtm180) REVERT: D 728 GLN cc_start: 0.8057 (tp40) cc_final: 0.7760 (tp-100) REVERT: D 781 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8435 (mt) outliers start: 48 outliers final: 28 residues processed: 186 average time/residue: 1.5557 time to fit residues: 312.3009 Evaluate side-chains 184 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 641 ARG Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 105 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN B 223 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14253 Z= 0.151 Angle : 0.550 9.610 19374 Z= 0.279 Chirality : 0.039 0.149 2265 Planarity : 0.004 0.045 2420 Dihedral : 6.890 76.856 2056 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.78 % Allowed : 12.97 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1746 helix: 1.74 (0.16), residues: 1102 sheet: -1.69 (2.00), residues: 5 loop : -1.85 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 524 HIS 0.003 0.001 HIS C 658 PHE 0.014 0.001 PHE C 329 TYR 0.011 0.001 TYR D 505 ARG 0.008 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.770 Fit side-chains REVERT: A 86 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5400 (tm-30) REVERT: A 167 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: A 201 GLU cc_start: 0.7000 (tp30) cc_final: 0.6661 (tp30) REVERT: B 110 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7640 (mpt-90) REVERT: B 148 MET cc_start: 0.7105 (mpp) cc_final: 0.6766 (mpp) REVERT: B 281 ASP cc_start: 0.7261 (t0) cc_final: 0.6941 (t0) REVERT: C 401 MET cc_start: 0.8336 (mmm) cc_final: 0.8134 (mmp) REVERT: C 617 GLU cc_start: 0.7354 (pt0) cc_final: 0.6973 (pm20) REVERT: C 628 ARG cc_start: 0.7610 (ttm110) cc_final: 0.7317 (ttm-80) REVERT: C 631 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7471 (pp-130) REVERT: C 717 ARG cc_start: 0.6923 (mpt180) cc_final: 0.5520 (mmt180) REVERT: D 97 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7335 (mt) REVERT: D 269 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7747 (mt) REVERT: D 571 MET cc_start: 0.8934 (mtp) cc_final: 0.8678 (mtp) REVERT: D 728 GLN cc_start: 0.8070 (tp40) cc_final: 0.7763 (tp-100) REVERT: D 781 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8411 (mt) outliers start: 42 outliers final: 21 residues processed: 185 average time/residue: 1.5807 time to fit residues: 316.6429 Evaluate side-chains 170 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 93 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14253 Z= 0.185 Angle : 0.581 10.050 19374 Z= 0.296 Chirality : 0.040 0.178 2265 Planarity : 0.004 0.047 2420 Dihedral : 7.013 77.638 2056 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.51 % Allowed : 13.50 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1746 helix: 1.80 (0.16), residues: 1095 sheet: -1.70 (1.98), residues: 5 loop : -1.85 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 524 HIS 0.004 0.001 HIS C 658 PHE 0.015 0.001 PHE C 329 TYR 0.014 0.001 TYR D 505 ARG 0.009 0.001 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 1.636 Fit side-chains REVERT: A 86 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5421 (tm-30) REVERT: A 160 GLU cc_start: 0.7119 (mp0) cc_final: 0.6796 (mp0) REVERT: A 167 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: A 201 GLU cc_start: 0.7036 (tp30) cc_final: 0.6667 (tp30) REVERT: B 110 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7649 (mpt-90) REVERT: B 148 MET cc_start: 0.7130 (mpp) cc_final: 0.6791 (mpp) REVERT: B 281 ASP cc_start: 0.7263 (t0) cc_final: 0.6950 (t0) REVERT: C 401 MET cc_start: 0.8317 (mmm) cc_final: 0.8110 (mmp) REVERT: C 617 GLU cc_start: 0.7374 (pt0) cc_final: 0.6991 (pm20) REVERT: C 628 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7317 (ttm-80) REVERT: C 631 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7551 (pp-130) REVERT: C 717 ARG cc_start: 0.7017 (mpt180) cc_final: 0.5575 (mmt180) REVERT: C 724 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 97 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7360 (mt) REVERT: D 269 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7761 (mt) REVERT: D 349 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6311 (tmt) REVERT: D 571 MET cc_start: 0.8961 (mtp) cc_final: 0.8696 (mtp) REVERT: D 641 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7802 (mtm180) REVERT: D 728 GLN cc_start: 0.8072 (tp40) cc_final: 0.7769 (tp-100) REVERT: D 730 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7687 (tt0) REVERT: D 781 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8471 (mt) outliers start: 38 outliers final: 23 residues processed: 173 average time/residue: 1.5664 time to fit residues: 293.3121 Evaluate side-chains 172 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 641 ARG Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 93 ASN B 223 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14253 Z= 0.163 Angle : 0.583 12.357 19374 Z= 0.292 Chirality : 0.040 0.215 2265 Planarity : 0.004 0.046 2420 Dihedral : 6.886 76.640 2056 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.04 % Allowed : 13.04 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1746 helix: 1.87 (0.16), residues: 1096 sheet: -1.72 (2.02), residues: 5 loop : -1.80 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 524 HIS 0.004 0.001 HIS C 658 PHE 0.015 0.001 PHE C 329 TYR 0.012 0.001 TYR D 505 ARG 0.008 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 1.745 Fit side-chains REVERT: A 86 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5400 (tm-30) REVERT: A 113 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: A 167 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: A 201 GLU cc_start: 0.7046 (tp30) cc_final: 0.6718 (tp30) REVERT: B 110 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7644 (mpt-90) REVERT: B 148 MET cc_start: 0.7094 (mpp) cc_final: 0.6754 (mpp) REVERT: B 281 ASP cc_start: 0.7251 (t0) cc_final: 0.6917 (t0) REVERT: C 401 MET cc_start: 0.8315 (mmm) cc_final: 0.8110 (mmp) REVERT: C 617 GLU cc_start: 0.7366 (pt0) cc_final: 0.6995 (pm20) REVERT: C 628 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7287 (ttm-80) REVERT: C 631 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7399 (pp-130) REVERT: C 717 ARG cc_start: 0.7005 (mpt180) cc_final: 0.5565 (mmt180) REVERT: C 724 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7814 (mp) REVERT: D 97 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7340 (mt) REVERT: D 269 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 332 MET cc_start: 0.8471 (mmm) cc_final: 0.8256 (mmm) REVERT: D 571 MET cc_start: 0.8939 (mtp) cc_final: 0.8685 (mtp) REVERT: D 588 MET cc_start: 0.8224 (mtp) cc_final: 0.7982 (mtm) REVERT: D 641 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7725 (mtm180) REVERT: D 728 GLN cc_start: 0.8067 (tp40) cc_final: 0.7786 (tp-100) REVERT: D 730 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7701 (tt0) REVERT: D 781 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8420 (mt) outliers start: 46 outliers final: 25 residues processed: 179 average time/residue: 1.5851 time to fit residues: 306.6317 Evaluate side-chains 174 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 641 ARG Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 0.3980 chunk 160 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14253 Z= 0.324 Angle : 0.696 12.035 19374 Z= 0.356 Chirality : 0.046 0.213 2265 Planarity : 0.005 0.053 2420 Dihedral : 7.671 81.300 2056 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.32 % Allowed : 13.77 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1746 helix: 1.55 (0.16), residues: 1089 sheet: -1.69 (2.09), residues: 5 loop : -1.91 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 524 HIS 0.005 0.001 HIS C 658 PHE 0.027 0.002 PHE D 613 TYR 0.024 0.002 TYR D 505 ARG 0.009 0.001 ARG C 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.764 Fit side-chains REVERT: A 86 GLU cc_start: 0.6239 (OUTLIER) cc_final: 0.5120 (tm-30) REVERT: A 160 GLU cc_start: 0.7219 (mp0) cc_final: 0.6922 (mp0) REVERT: A 167 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: A 201 GLU cc_start: 0.7126 (tp30) cc_final: 0.6798 (tp30) REVERT: B 110 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7656 (mpt-90) REVERT: B 148 MET cc_start: 0.7104 (mpp) cc_final: 0.6863 (mpp) REVERT: B 281 ASP cc_start: 0.7275 (t0) cc_final: 0.6912 (t0) REVERT: C 617 GLU cc_start: 0.7502 (pt0) cc_final: 0.7016 (pm20) REVERT: C 628 ARG cc_start: 0.7578 (ttm110) cc_final: 0.7300 (ttm-80) REVERT: C 631 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7533 (pp-130) REVERT: C 717 ARG cc_start: 0.7227 (mpt180) cc_final: 0.5581 (mmt180) REVERT: C 724 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7806 (mp) REVERT: D 97 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 269 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7871 (mt) REVERT: D 332 MET cc_start: 0.8456 (mmm) cc_final: 0.8209 (mmm) REVERT: D 728 GLN cc_start: 0.8065 (tp40) cc_final: 0.7798 (tp-100) REVERT: D 730 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7748 (tt0) REVERT: D 775 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7699 (ttp80) outliers start: 35 outliers final: 23 residues processed: 177 average time/residue: 1.5627 time to fit residues: 300.9125 Evaluate side-chains 173 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 775 ARG Chi-restraints excluded: chain D residue 781 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 93 ASN B 223 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107868 restraints weight = 16922.983| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.47 r_work: 0.3143 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14253 Z= 0.160 Angle : 0.585 11.465 19374 Z= 0.297 Chirality : 0.040 0.200 2265 Planarity : 0.004 0.046 2420 Dihedral : 7.160 77.136 2056 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.25 % Allowed : 14.10 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1746 helix: 1.82 (0.16), residues: 1097 sheet: -1.57 (2.17), residues: 5 loop : -1.87 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 524 HIS 0.004 0.001 HIS C 658 PHE 0.015 0.001 PHE C 329 TYR 0.012 0.001 TYR D 505 ARG 0.007 0.000 ARG C 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5585.10 seconds wall clock time: 99 minutes 19.01 seconds (5959.01 seconds total)