Starting phenix.real_space_refine on Mon Apr 15 23:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/04_2024/7yux_34114_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 126 5.16 5 C 23078 2.51 5 N 6427 2.21 5 O 6944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 656": "OD1" <-> "OD2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "E GLU 705": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 434": "OD1" <-> "OD2" Residue "D PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36585 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.89, per 1000 atoms: 0.49 Number of scatterers: 36585 At special positions: 0 Unit cell: (174.66, 155.8, 179.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 10 15.00 O 6944 8.00 N 6427 7.00 C 23078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.17 Conformation dependent library (CDL) restraints added in 7.1 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 36 sheets defined 40.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.25 Creating SS restraints... Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 187 through 236 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.733A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 243' Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.609A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.688A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.798A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 445 through 450' Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 574 through 577 No H-bonds generated for 'chain 'A' and resid 574 through 577' Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 680 through 692 removed outlier: 3.615A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 740 through 744 removed outlier: 4.159A pdb=" N GLU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 744' Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 762 through 768 Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 158 through 167 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 185 through 236 removed outlier: 4.781A pdb=" N LYS C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.818A pdb=" N LYS C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.895A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 309 through 317 removed outlier: 3.836A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.510A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 541 through 559 Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.796A pdb=" N ILE C 574 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Proline residue: C 575 - end of helix No H-bonds generated for 'chain 'C' and resid 571 through 577' Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 728 removed outlier: 3.930A pdb=" N ALA C 728 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 742 through 745 Processing helix chain 'C' and resid 748 through 752 Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.761A pdb=" N ARG E 32 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.883A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER E 141 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 186 through 233 Processing helix chain 'E' and resid 240 through 255 removed outlier: 4.291A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.708A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 removed outlier: 4.336A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 436 through 443 Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 479 through 482 No H-bonds generated for 'chain 'E' and resid 479 through 482' Processing helix chain 'E' and resid 495 through 504 Processing helix chain 'E' and resid 506 through 514 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 574 through 578 Processing helix chain 'E' and resid 631 through 645 Processing helix chain 'E' and resid 680 through 692 Processing helix chain 'E' and resid 718 through 727 removed outlier: 3.510A pdb=" N HIS E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 762 through 767 Processing helix chain 'D' and resid 28 through 39 removed outlier: 4.201A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 185 through 233 Processing helix chain 'D' and resid 244 through 254 removed outlier: 3.635A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.586A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 4.224A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.633A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 338 Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 442 Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 495 through 505 removed outlier: 3.599A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 514 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 559 Processing helix chain 'D' and resid 574 through 577 No H-bonds generated for 'chain 'D' and resid 574 through 577' Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.560A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 743 through 745 No H-bonds generated for 'chain 'D' and resid 743 through 745' Processing helix chain 'D' and resid 748 through 753 Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.835A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.562A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 138 Processing helix chain 'F' and resid 146 through 152 removed outlier: 3.939A pdb=" N VAL F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 Processing helix chain 'F' and resid 173 through 181 Processing helix chain 'F' and resid 185 through 234 removed outlier: 3.915A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.928A pdb=" N GLU F 247 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 252 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 253 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU F 255 " --> pdb=" O LYS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 271 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 362 through 371 Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 435 through 443 Processing helix chain 'F' and resid 480 through 482 No H-bonds generated for 'chain 'F' and resid 480 through 482' Processing helix chain 'F' and resid 495 through 504 Processing helix chain 'F' and resid 506 through 514 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 542 through 559 Processing helix chain 'F' and resid 574 through 577 No H-bonds generated for 'chain 'F' and resid 574 through 577' Processing helix chain 'F' and resid 631 through 646 Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 680 through 692 Processing helix chain 'F' and resid 718 through 727 Processing helix chain 'F' and resid 737 through 744 removed outlier: 4.407A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 751 No H-bonds generated for 'chain 'F' and resid 748 through 751' Processing helix chain 'F' and resid 762 through 766 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 119 through 136 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.236A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.619A pdb=" N VAL B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 186 through 233 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 325 through 338 removed outlier: 4.107A pdb=" N GLU B 331 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B 332 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU B 333 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 387 through 391 removed outlier: 3.700A pdb=" N ARG B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.969A pdb=" N ASN B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 450' Processing helix chain 'B' and resid 474 through 476 No H-bonds generated for 'chain 'B' and resid 474 through 476' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 495 through 504 removed outlier: 3.686A pdb=" N GLN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 572 through 577 Proline residue: B 575 - end of helix No H-bonds generated for 'chain 'B' and resid 572 through 577' Processing helix chain 'B' and resid 631 through 647 removed outlier: 3.503A pdb=" N HIS B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 745 removed outlier: 4.437A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 8.392A pdb=" N ILE A 8 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 45 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU A 10 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 47 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 376 through 380 removed outlier: 6.901A pdb=" N VAL A 418 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE A 379 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 420 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.488A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 597 through 603 Processing sheet with id= E, first strand: chain 'A' and resid 613 through 618 removed outlier: 3.748A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 736 removed outlier: 6.999A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 7 through 9 removed outlier: 7.031A pdb=" N PHE C 45 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.752A pdb=" N GLN C 73 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 469 through 471 Processing sheet with id= J, first strand: chain 'C' and resid 520 through 522 removed outlier: 7.328A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 596 through 603 removed outlier: 3.505A pdb=" N ALA C 601 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 732 through 736 removed outlier: 6.371A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.666A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 376 through 380 removed outlier: 6.640A pdb=" N VAL E 418 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE E 379 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU E 420 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU E 421 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE E 468 " --> pdb=" O LEU E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 520 through 522 removed outlier: 5.584A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 613 through 618 Processing sheet with id= Q, first strand: chain 'E' and resid 732 through 736 removed outlier: 6.166A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= S, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.905A pdb=" N MET D 85 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU D 87 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N VAL D 71 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 488 through 490 removed outlier: 8.914A pdb=" N LEU D 353 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR D 469 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY D 355 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA D 471 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 379 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.077A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.595A pdb=" N GLY D 599 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.932A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.454A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.939A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 87 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 352 through 354 removed outlier: 8.974A pdb=" N LEU F 353 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR F 469 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 520 through 522 removed outlier: 5.695A pdb=" N ARG F 567 " --> pdb=" O GLU F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 596 through 601 Processing sheet with id= AC, first strand: chain 'F' and resid 732 through 736 removed outlier: 5.815A pdb=" N GLU F 755 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU F 735 " --> pdb=" O GLU F 755 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS F 757 " --> pdb=" O LEU F 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.725A pdb=" N PHE B 45 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 10 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 47 " --> pdb=" O LEU B 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'B' and resid 65 through 67 Processing sheet with id= AF, first strand: chain 'B' and resid 352 through 354 removed outlier: 7.814A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 597 through 601 removed outlier: 4.095A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 614 through 617 removed outlier: 3.690A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 617 " --> pdb=" O ASP B 662 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.550A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'B' and resid 70 through 73 removed outlier: 6.928A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) 1315 hydrogen bonds defined for protein. 3759 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: 13.12 Time building geometry restraints manager: 14.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12210 1.34 - 1.46: 4302 1.46 - 1.58: 20469 1.58 - 1.70: 16 1.70 - 1.81: 252 Bond restraints: 37249 Sorted by residual: bond pdb=" C ILE B 233 " pdb=" O ILE B 233 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.19e-02 7.06e+03 7.83e+01 bond pdb=" N ILE D 233 " pdb=" CA ILE D 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.07e-02 8.73e+03 1.21e+01 bond pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.36e+00 bond pdb=" N LEU D 237 " pdb=" CA LEU D 237 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.01e+00 bond pdb=" N GLU F 240 " pdb=" CA GLU F 240 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.26e-02 6.30e+03 8.86e+00 ... (remaining 37244 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.97: 1122 105.97 - 113.58: 20975 113.58 - 121.20: 18221 121.20 - 128.82: 9953 128.82 - 136.43: 234 Bond angle restraints: 50505 Sorted by residual: angle pdb=" N VAL C 605 " pdb=" CA VAL C 605 " pdb=" C VAL C 605 " ideal model delta sigma weight residual 111.91 106.23 5.68 8.90e-01 1.26e+00 4.07e+01 angle pdb=" N ILE D 233 " pdb=" CA ILE D 233 " pdb=" C ILE D 233 " ideal model delta sigma weight residual 113.10 108.01 5.09 9.70e-01 1.06e+00 2.75e+01 angle pdb=" C LYS B 235 " pdb=" CA LYS B 235 " pdb=" CB LYS B 235 " ideal model delta sigma weight residual 110.06 117.47 -7.41 1.44e+00 4.82e-01 2.65e+01 angle pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" O LEU B 243 " ideal model delta sigma weight residual 121.84 116.28 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N GLU B 247 " pdb=" CA GLU B 247 " pdb=" C GLU B 247 " ideal model delta sigma weight residual 111.96 105.39 6.57 1.41e+00 5.03e-01 2.17e+01 ... (remaining 50500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 22653 35.28 - 70.57: 278 70.57 - 105.85: 39 105.85 - 141.13: 7 141.13 - 176.42: 4 Dihedral angle restraints: 22981 sinusoidal: 9595 harmonic: 13386 Sorted by residual: dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 dihedral pdb=" CA ASP F 51 " pdb=" C ASP F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta harmonic sigma weight residual -180.00 -134.73 -45.27 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -142.33 -37.67 0 5.00e+00 4.00e-02 5.68e+01 ... (remaining 22978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4730 0.058 - 0.116: 904 0.116 - 0.173: 97 0.173 - 0.231: 9 0.231 - 0.289: 4 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CA ASP B 241 " pdb=" N ASP B 241 " pdb=" C ASP B 241 " pdb=" CB ASP B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU F 237 " pdb=" N LEU F 237 " pdb=" C LEU F 237 " pdb=" CB LEU F 237 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS B 235 " pdb=" N LYS B 235 " pdb=" C LYS B 235 " pdb=" CB LYS B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 5741 not shown) Planarity restraints: 6557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " 0.028 2.00e-02 2.50e+03 5.55e-02 3.09e+01 pdb=" C ILE B 233 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE B 233 " 0.034 2.00e-02 2.50e+03 pdb=" N GLN B 234 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 667 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 668 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 668 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 668 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.018 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B 602 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.003 2.00e-02 2.50e+03 ... (remaining 6554 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 476 2.64 - 3.20: 34388 3.20 - 3.77: 58405 3.77 - 4.33: 78900 4.33 - 4.90: 125812 Nonbonded interactions: 297981 Sorted by model distance: nonbonded pdb=" OG1 THR C 603 " pdb=" O GLY C 606 " model vdw 2.071 2.440 nonbonded pdb=" OE1 GLN C 277 " pdb=" OG1 THR C 284 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR E 603 " pdb=" O GLY E 606 " model vdw 2.128 2.440 nonbonded pdb=" OD1 ASP A 218 " pdb=" NH1 ARG D 198 " model vdw 2.129 2.520 nonbonded pdb=" OG1 THR F 603 " pdb=" O GLY F 606 " model vdw 2.141 2.440 ... (remaining 297976 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 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) selection = (chain 'D' and resid 2 through 774) selection = (chain 'E' and resid 2 through 774) 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.040 Extract box with map and model: 10.170 Check model and map are aligned: 0.500 Set scattering table: 0.350 Process input model: 90.910 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.220 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 37249 Z= 0.205 Angle : 0.698 9.627 50505 Z= 0.383 Chirality : 0.045 0.289 5744 Planarity : 0.005 0.104 6557 Dihedral : 13.368 176.416 14365 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 0.26 % Allowed : 0.41 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4626 helix: 0.59 (0.12), residues: 1937 sheet: -2.16 (0.21), residues: 547 loop : -1.54 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 602 HIS 0.005 0.001 HIS F 407 PHE 0.012 0.001 PHE A 657 TYR 0.028 0.001 TYR F 63 ARG 0.008 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 4.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6426 (tpt) cc_final: 0.5617 (mpp) REVERT: A 682 THR cc_start: 0.8254 (m) cc_final: 0.7980 (p) REVERT: C 425 ASP cc_start: 0.8830 (p0) cc_final: 0.8355 (p0) REVERT: C 473 THR cc_start: 0.8152 (m) cc_final: 0.7878 (p) REVERT: E 241 ASP cc_start: 0.2392 (OUTLIER) cc_final: 0.1345 (m-30) REVERT: E 243 LEU cc_start: 0.5995 (tp) cc_final: 0.5573 (mt) REVERT: E 512 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6368 (tpt90) REVERT: E 563 TRP cc_start: 0.5276 (p90) cc_final: 0.4328 (p90) REVERT: D 625 LEU cc_start: 0.7625 (mp) cc_final: 0.7275 (mp) REVERT: F 218 ASP cc_start: 0.7849 (m-30) cc_final: 0.7613 (p0) REVERT: F 427 MET cc_start: 0.3069 (mmp) cc_final: 0.2139 (mmp) REVERT: F 439 MET cc_start: 0.6887 (mtt) cc_final: 0.6662 (mtp) REVERT: F 496 MET cc_start: 0.7729 (tpt) cc_final: 0.7378 (tpt) REVERT: F 633 MET cc_start: 0.8264 (mpp) cc_final: 0.7708 (mpp) REVERT: B 171 TRP cc_start: 0.0010 (p90) cc_final: -0.0234 (p90) REVERT: B 245 ASP cc_start: 0.5926 (m-30) cc_final: 0.5712 (m-30) REVERT: B 386 ASP cc_start: 0.8497 (p0) cc_final: 0.7867 (p0) REVERT: B 476 THR cc_start: 0.8308 (t) cc_final: 0.7021 (m) outliers start: 10 outliers final: 4 residues processed: 435 average time/residue: 0.4551 time to fit residues: 331.5448 Evaluate side-chains 322 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 317 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 40.0000 chunk 350 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 269 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 220 ASN A 319 HIS C 83 GLN C 278 GLN D 277 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 37249 Z= 0.341 Angle : 0.721 10.136 50505 Z= 0.356 Chirality : 0.046 0.213 5744 Planarity : 0.006 0.072 6557 Dihedral : 8.907 173.984 5172 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 1.57 % Allowed : 8.89 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.12), residues: 4626 helix: 0.29 (0.12), residues: 1969 sheet: -2.26 (0.21), residues: 541 loop : -1.75 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 602 HIS 0.010 0.002 HIS C 407 PHE 0.025 0.002 PHE B 466 TYR 0.023 0.002 TYR A 493 ARG 0.011 0.001 ARG F 519 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 336 time to evaluate : 4.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6364 (tpt) cc_final: 0.5526 (mpp) REVERT: A 713 MET cc_start: 0.6461 (tmm) cc_final: 0.5612 (tmm) REVERT: C 425 ASP cc_start: 0.8897 (p0) cc_final: 0.8466 (p0) REVERT: C 735 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7931 (mp) REVERT: E 563 TRP cc_start: 0.5430 (p90) cc_final: 0.4682 (p90) REVERT: E 620 SER cc_start: 0.7936 (m) cc_final: 0.7524 (t) REVERT: E 764 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7060 (mt-10) REVERT: D 401 MET cc_start: 0.6641 (tpp) cc_final: 0.6403 (tpp) REVERT: D 625 LEU cc_start: 0.7784 (mp) cc_final: 0.7505 (mp) REVERT: F 439 MET cc_start: 0.6828 (mtt) cc_final: 0.6611 (mtp) REVERT: F 496 MET cc_start: 0.7698 (tpt) cc_final: 0.7336 (tpt) REVERT: F 633 MET cc_start: 0.8702 (mpp) cc_final: 0.8107 (mpp) REVERT: F 683 MET cc_start: 0.8279 (mtp) cc_final: 0.7933 (mtp) REVERT: B 386 ASP cc_start: 0.8719 (p0) cc_final: 0.7948 (p0) REVERT: B 516 MET cc_start: 0.7267 (ttm) cc_final: 0.7061 (ttm) outliers start: 61 outliers final: 40 residues processed: 374 average time/residue: 0.4548 time to fit residues: 287.0759 Evaluate side-chains 351 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 310 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 675 ASP Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 285 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 420 optimal weight: 1.9990 chunk 454 optimal weight: 3.9990 chunk 374 optimal weight: 20.0000 chunk 416 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 337 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37249 Z= 0.204 Angle : 0.613 8.919 50505 Z= 0.299 Chirality : 0.043 0.186 5744 Planarity : 0.005 0.060 6557 Dihedral : 8.496 177.549 5164 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.66 % Favored : 93.32 % Rotamer: Outliers : 1.59 % Allowed : 11.86 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 4626 helix: 0.52 (0.12), residues: 1962 sheet: -2.13 (0.21), residues: 553 loop : -1.63 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 431 HIS 0.006 0.001 HIS C 647 PHE 0.015 0.001 PHE F 657 TYR 0.022 0.001 TYR D 332 ARG 0.005 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 330 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6408 (tpt) cc_final: 0.5540 (mpp) REVERT: A 713 MET cc_start: 0.6564 (tmm) cc_final: 0.5696 (tmm) REVERT: A 723 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6292 (mt) REVERT: C 160 MET cc_start: -0.0981 (mpp) cc_final: -0.1211 (mpp) REVERT: C 425 ASP cc_start: 0.8772 (p0) cc_final: 0.8127 (p0) REVERT: C 440 LEU cc_start: 0.8021 (tp) cc_final: 0.7706 (mt) REVERT: C 473 THR cc_start: 0.8487 (m) cc_final: 0.8135 (m) REVERT: C 735 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7797 (mp) REVERT: E 563 TRP cc_start: 0.5402 (p90) cc_final: 0.4711 (p90) REVERT: E 620 SER cc_start: 0.7831 (m) cc_final: 0.7487 (t) REVERT: D 228 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8012 (tm-30) REVERT: D 251 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8134 (pttm) REVERT: D 625 LEU cc_start: 0.7702 (mp) cc_final: 0.7475 (mp) REVERT: F 633 MET cc_start: 0.8699 (mpp) cc_final: 0.8142 (mpp) REVERT: F 641 LEU cc_start: 0.8894 (mt) cc_final: 0.8674 (mt) REVERT: F 683 MET cc_start: 0.8359 (mtp) cc_final: 0.8056 (mtp) REVERT: B 241 ASP cc_start: 0.6304 (OUTLIER) cc_final: 0.5699 (p0) REVERT: B 386 ASP cc_start: 0.8660 (p0) cc_final: 0.7869 (p0) outliers start: 62 outliers final: 42 residues processed: 376 average time/residue: 0.4586 time to fit residues: 292.9183 Evaluate side-chains 358 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 313 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 8.9990 chunk 316 optimal weight: 50.0000 chunk 218 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 421 optimal weight: 4.9990 chunk 446 optimal weight: 0.0870 chunk 220 optimal weight: 6.9990 chunk 399 optimal weight: 40.0000 chunk 120 optimal weight: 9.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 310 HIS A 340 GLN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS E 666 HIS D 18 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 37249 Z= 0.346 Angle : 0.706 10.101 50505 Z= 0.346 Chirality : 0.045 0.256 5744 Planarity : 0.005 0.073 6557 Dihedral : 8.678 176.295 5164 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 2.57 % Allowed : 13.66 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4626 helix: 0.26 (0.12), residues: 1968 sheet: -2.23 (0.21), residues: 545 loop : -1.75 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.010 0.002 HIS C 647 PHE 0.037 0.002 PHE F 557 TYR 0.035 0.002 TYR A 493 ARG 0.007 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 317 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6337 (tpt) cc_final: 0.5460 (mpp) REVERT: A 713 MET cc_start: 0.6722 (tmm) cc_final: 0.5899 (tmm) REVERT: A 723 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6724 (mt) REVERT: C 160 MET cc_start: -0.0936 (mpp) cc_final: -0.1158 (mpp) REVERT: C 230 MET cc_start: 0.5258 (mpp) cc_final: 0.4964 (mpp) REVERT: C 528 LEU cc_start: 0.8536 (pp) cc_final: 0.8162 (tt) REVERT: C 683 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: C 733 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7675 (mm) REVERT: C 735 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7866 (mp) REVERT: E 563 TRP cc_start: 0.5550 (p90) cc_final: 0.4848 (p90) REVERT: E 620 SER cc_start: 0.7996 (m) cc_final: 0.7632 (t) REVERT: D 228 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7972 (tm-30) REVERT: D 251 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8162 (pttm) REVERT: D 401 MET cc_start: 0.6678 (tpp) cc_final: 0.6084 (tpp) REVERT: F 75 MET cc_start: 0.4779 (tmm) cc_final: 0.4537 (tmm) REVERT: F 633 MET cc_start: 0.8754 (mpp) cc_final: 0.8173 (mpp) REVERT: B 211 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7898 (mm-40) REVERT: B 386 ASP cc_start: 0.8703 (p0) cc_final: 0.7889 (p0) outliers start: 100 outliers final: 68 residues processed: 387 average time/residue: 0.4495 time to fit residues: 295.9425 Evaluate side-chains 372 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 300 time to evaluate : 3.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 chunk 381 optimal weight: 4.9990 chunk 308 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 228 optimal weight: 0.0870 chunk 400 optimal weight: 50.0000 chunk 112 optimal weight: 0.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37249 Z= 0.265 Angle : 0.653 10.067 50505 Z= 0.318 Chirality : 0.044 0.225 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.575 176.882 5164 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 2.75 % Allowed : 15.49 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.33 (0.12), residues: 4626 helix: 0.37 (0.12), residues: 1968 sheet: -2.16 (0.21), residues: 545 loop : -1.72 (0.14), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 563 HIS 0.007 0.001 HIS E 377 PHE 0.017 0.002 PHE B 466 TYR 0.028 0.002 TYR A 493 ARG 0.007 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 321 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6321 (tpt) cc_final: 0.5436 (mpp) REVERT: A 713 MET cc_start: 0.6706 (tmm) cc_final: 0.5874 (tmm) REVERT: A 723 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6702 (mt) REVERT: C 160 MET cc_start: -0.0957 (mpp) cc_final: -0.1199 (mpp) REVERT: C 230 MET cc_start: 0.5287 (mpp) cc_final: 0.5041 (mpp) REVERT: C 425 ASP cc_start: 0.8733 (p0) cc_final: 0.8034 (p0) REVERT: C 473 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8175 (m) REVERT: C 735 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7795 (mp) REVERT: E 563 TRP cc_start: 0.5534 (p90) cc_final: 0.4383 (p90) REVERT: E 620 SER cc_start: 0.7947 (m) cc_final: 0.7565 (t) REVERT: D 228 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 251 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8188 (pttm) REVERT: F 443 LEU cc_start: 0.7183 (tp) cc_final: 0.6949 (tp) REVERT: F 485 MET cc_start: 0.6424 (mmm) cc_final: 0.6168 (mmp) REVERT: F 633 MET cc_start: 0.8753 (mpp) cc_final: 0.8189 (mpp) REVERT: F 641 LEU cc_start: 0.8898 (mt) cc_final: 0.8660 (mt) REVERT: B 85 MET cc_start: 0.1038 (mmt) cc_final: 0.0643 (tmm) REVERT: B 386 ASP cc_start: 0.8728 (p0) cc_final: 0.7855 (p0) REVERT: B 475 GLN cc_start: 0.7247 (mp10) cc_final: 0.6413 (mt0) REVERT: B 527 ILE cc_start: 0.8813 (mm) cc_final: 0.8529 (mm) outliers start: 107 outliers final: 79 residues processed: 392 average time/residue: 0.4718 time to fit residues: 315.1281 Evaluate side-chains 382 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 300 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.5980 chunk 402 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 234 optimal weight: 30.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS D 659 ASN ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 37249 Z= 0.255 Angle : 0.654 11.383 50505 Z= 0.316 Chirality : 0.044 0.229 5744 Planarity : 0.005 0.073 6557 Dihedral : 8.522 177.242 5164 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.43 % Rotamer: Outliers : 3.11 % Allowed : 16.10 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.26 (0.13), residues: 4626 helix: 0.43 (0.12), residues: 1964 sheet: -2.14 (0.22), residues: 526 loop : -1.67 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 431 HIS 0.007 0.001 HIS E 377 PHE 0.042 0.002 PHE F 557 TYR 0.025 0.002 TYR A 493 ARG 0.007 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 312 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6325 (tpt) cc_final: 0.5440 (mpp) REVERT: A 713 MET cc_start: 0.6682 (tmm) cc_final: 0.5841 (tmm) REVERT: A 723 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6543 (mt) REVERT: C 160 MET cc_start: -0.1044 (mpp) cc_final: -0.1281 (mpp) REVERT: C 230 MET cc_start: 0.5278 (mpp) cc_final: 0.4948 (mpp) REVERT: C 512 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7735 (ptp90) REVERT: C 730 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7832 (tt) REVERT: C 735 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7807 (mp) REVERT: E 273 LEU cc_start: 0.7976 (mt) cc_final: 0.7700 (mt) REVERT: E 563 TRP cc_start: 0.5575 (p90) cc_final: 0.4652 (p90) REVERT: E 620 SER cc_start: 0.7923 (m) cc_final: 0.7574 (t) REVERT: D 228 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8110 (tm-30) REVERT: D 251 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8194 (pttm) REVERT: D 401 MET cc_start: 0.6711 (tpp) cc_final: 0.6170 (tpp) REVERT: D 427 MET cc_start: 0.8212 (mtp) cc_final: 0.7923 (mtp) REVERT: F 75 MET cc_start: 0.4625 (tmm) cc_final: 0.4403 (tmm) REVERT: F 633 MET cc_start: 0.8740 (mpp) cc_final: 0.8178 (mpp) REVERT: F 641 LEU cc_start: 0.8884 (mt) cc_final: 0.8660 (mt) REVERT: B 85 MET cc_start: 0.0892 (mmt) cc_final: 0.0487 (tmm) REVERT: B 386 ASP cc_start: 0.8700 (p0) cc_final: 0.7848 (p0) REVERT: B 475 GLN cc_start: 0.7243 (mp10) cc_final: 0.6502 (mt0) REVERT: B 527 ILE cc_start: 0.8787 (mm) cc_final: 0.8501 (mm) outliers start: 121 outliers final: 96 residues processed: 398 average time/residue: 0.4569 time to fit residues: 307.7511 Evaluate side-chains 405 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 305 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 326 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 249 optimal weight: 40.0000 chunk 445 optimal weight: 3.9990 chunk 278 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 220 ASN A 234 GLN A 310 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37249 Z= 0.219 Angle : 0.637 10.638 50505 Z= 0.306 Chirality : 0.043 0.219 5744 Planarity : 0.005 0.066 6557 Dihedral : 8.405 178.665 5164 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 2.85 % Allowed : 16.62 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.13 (0.13), residues: 4626 helix: 0.53 (0.12), residues: 1972 sheet: -2.01 (0.22), residues: 520 loop : -1.63 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 558 HIS 0.006 0.001 HIS E 377 PHE 0.016 0.001 PHE F 657 TYR 0.024 0.001 TYR D 332 ARG 0.006 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 322 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6379 (tpt) cc_final: 0.5500 (mpp) REVERT: A 702 MET cc_start: 0.4667 (mtt) cc_final: 0.4397 (mtt) REVERT: A 713 MET cc_start: 0.6669 (tmm) cc_final: 0.5839 (tmm) REVERT: A 723 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6598 (mt) REVERT: C 230 MET cc_start: 0.5354 (mpp) cc_final: 0.5037 (mpp) REVERT: C 440 LEU cc_start: 0.8139 (tp) cc_final: 0.7674 (mt) REVERT: C 512 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7800 (ptp90) REVERT: C 735 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7770 (mp) REVERT: E 273 LEU cc_start: 0.8042 (mt) cc_final: 0.7766 (mt) REVERT: E 563 TRP cc_start: 0.5534 (p90) cc_final: 0.4650 (p90) REVERT: E 620 SER cc_start: 0.7888 (m) cc_final: 0.7521 (t) REVERT: D 228 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 251 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8188 (pttm) REVERT: D 427 MET cc_start: 0.8183 (mtp) cc_final: 0.7917 (mtp) REVERT: F 75 MET cc_start: 0.4530 (tmm) cc_final: 0.4287 (tmm) REVERT: F 431 TRP cc_start: 0.4642 (t-100) cc_final: 0.3920 (t60) REVERT: F 443 LEU cc_start: 0.7135 (tp) cc_final: 0.6896 (tp) REVERT: F 485 MET cc_start: 0.6221 (mmm) cc_final: 0.5871 (mmp) REVERT: F 633 MET cc_start: 0.8738 (mpp) cc_final: 0.8202 (mpp) REVERT: B 85 MET cc_start: 0.0691 (mmt) cc_final: 0.0299 (tmm) REVERT: B 386 ASP cc_start: 0.8704 (p0) cc_final: 0.7892 (p0) REVERT: B 475 GLN cc_start: 0.7179 (mp10) cc_final: 0.6571 (mt0) REVERT: B 527 ILE cc_start: 0.8766 (mm) cc_final: 0.8497 (mm) outliers start: 111 outliers final: 87 residues processed: 401 average time/residue: 0.4669 time to fit residues: 315.1912 Evaluate side-chains 403 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 313 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 0.8980 chunk 177 optimal weight: 0.0670 chunk 265 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 283 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** C 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS F 510 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37249 Z= 0.163 Angle : 0.614 11.443 50505 Z= 0.293 Chirality : 0.043 0.262 5744 Planarity : 0.004 0.070 6557 Dihedral : 8.172 177.907 5164 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.90 % Favored : 94.08 % Rotamer: Outliers : 2.29 % Allowed : 17.10 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.87 (0.13), residues: 4626 helix: 0.77 (0.12), residues: 1960 sheet: -1.86 (0.22), residues: 538 loop : -1.50 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 558 HIS 0.005 0.001 HIS E 666 PHE 0.009 0.001 PHE B 376 TYR 0.022 0.001 TYR F 63 ARG 0.009 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 338 time to evaluate : 4.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6494 (tpt) cc_final: 0.5608 (mpp) REVERT: A 682 THR cc_start: 0.7707 (m) cc_final: 0.7439 (p) REVERT: A 702 MET cc_start: 0.4427 (mtt) cc_final: 0.4205 (mtt) REVERT: A 713 MET cc_start: 0.6719 (tmm) cc_final: 0.5891 (tmm) REVERT: A 723 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6393 (mt) REVERT: C 230 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.5127 (mpp) REVERT: C 440 LEU cc_start: 0.8017 (tp) cc_final: 0.7544 (mt) REVERT: C 735 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7572 (mp) REVERT: E 273 LEU cc_start: 0.8077 (mt) cc_final: 0.7805 (mt) REVERT: E 422 ASP cc_start: 0.7063 (m-30) cc_final: 0.6718 (m-30) REVERT: E 563 TRP cc_start: 0.5475 (p90) cc_final: 0.4695 (p90) REVERT: E 620 SER cc_start: 0.7743 (m) cc_final: 0.7416 (t) REVERT: D 251 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8186 (pttm) REVERT: D 401 MET cc_start: 0.6336 (tpp) cc_final: 0.5707 (tpp) REVERT: D 427 MET cc_start: 0.8150 (mtp) cc_final: 0.7889 (mtp) REVERT: F 2 ARG cc_start: 0.3205 (mmt180) cc_final: 0.2957 (mmm160) REVERT: F 75 MET cc_start: 0.4425 (tmm) cc_final: 0.4165 (tmm) REVERT: F 416 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8065 (p0) REVERT: F 431 TRP cc_start: 0.4547 (t-100) cc_final: 0.3862 (t60) REVERT: F 633 MET cc_start: 0.8721 (mpp) cc_final: 0.8465 (ptp) REVERT: B 85 MET cc_start: 0.0527 (mmt) cc_final: 0.0108 (tmm) REVERT: B 386 ASP cc_start: 0.8616 (p0) cc_final: 0.7833 (p0) REVERT: B 475 GLN cc_start: 0.7050 (mp10) cc_final: 0.6479 (mt0) outliers start: 89 outliers final: 69 residues processed: 396 average time/residue: 0.5054 time to fit residues: 338.8973 Evaluate side-chains 389 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 316 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 20.0000 chunk 426 optimal weight: 5.9990 chunk 389 optimal weight: 0.6980 chunk 414 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 325 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 374 optimal weight: 9.9990 chunk 392 optimal weight: 30.0000 chunk 413 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS E 664 HIS E 666 HIS F 638 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37249 Z= 0.177 Angle : 0.634 14.856 50505 Z= 0.299 Chirality : 0.043 0.211 5744 Planarity : 0.005 0.077 6557 Dihedral : 8.108 177.150 5164 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.07 % Favored : 93.90 % Rotamer: Outliers : 2.16 % Allowed : 17.69 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.81 (0.13), residues: 4626 helix: 0.83 (0.12), residues: 1952 sheet: -1.81 (0.22), residues: 543 loop : -1.47 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 558 HIS 0.005 0.001 HIS E 377 PHE 0.045 0.001 PHE F 557 TYR 0.034 0.001 TYR B 768 ARG 0.015 0.000 ARG C 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 327 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6536 (tpt) cc_final: 0.5655 (mpp) REVERT: A 479 ARG cc_start: 0.4984 (ptt-90) cc_final: 0.4693 (ptt90) REVERT: A 698 MET cc_start: 0.2283 (mmt) cc_final: 0.1697 (mmt) REVERT: A 702 MET cc_start: 0.4439 (mtt) cc_final: 0.4197 (mtt) REVERT: A 713 MET cc_start: 0.6745 (tmm) cc_final: 0.5897 (tmm) REVERT: A 723 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6399 (mt) REVERT: C 230 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.5068 (mpp) REVERT: C 735 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7602 (mp) REVERT: E 273 LEU cc_start: 0.8006 (mt) cc_final: 0.7770 (mt) REVERT: E 422 ASP cc_start: 0.7147 (m-30) cc_final: 0.6771 (m-30) REVERT: E 543 LEU cc_start: 0.8006 (mt) cc_final: 0.7738 (tt) REVERT: E 563 TRP cc_start: 0.5487 (p90) cc_final: 0.4815 (p90) REVERT: E 620 SER cc_start: 0.7750 (m) cc_final: 0.7419 (t) REVERT: D 251 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8192 (pttm) REVERT: D 401 MET cc_start: 0.6310 (tpp) cc_final: 0.5740 (tpp) REVERT: D 427 MET cc_start: 0.8153 (mtp) cc_final: 0.7908 (mtp) REVERT: D 698 MET cc_start: 0.3587 (mmm) cc_final: 0.3332 (mmt) REVERT: F 2 ARG cc_start: 0.3240 (mmt180) cc_final: 0.2983 (mmm160) REVERT: F 75 MET cc_start: 0.4477 (tmm) cc_final: 0.4213 (tmm) REVERT: F 409 MET cc_start: 0.7668 (mpp) cc_final: 0.7403 (mpp) REVERT: F 431 TRP cc_start: 0.4584 (t-100) cc_final: 0.3913 (t60) REVERT: B 85 MET cc_start: 0.0434 (mmt) cc_final: -0.0039 (tmm) REVERT: B 386 ASP cc_start: 0.8601 (p0) cc_final: 0.7830 (p0) REVERT: B 475 GLN cc_start: 0.6966 (mp10) cc_final: 0.6618 (mt0) outliers start: 84 outliers final: 69 residues processed: 383 average time/residue: 0.5012 time to fit residues: 325.6742 Evaluate side-chains 390 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 2.9990 chunk 438 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 305 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 423 optimal weight: 3.9990 chunk 366 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS E 666 HIS F 510 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 37249 Z= 0.260 Angle : 0.678 12.985 50505 Z= 0.325 Chirality : 0.044 0.223 5744 Planarity : 0.005 0.073 6557 Dihedral : 8.272 177.970 5164 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.50 % Favored : 92.48 % Rotamer: Outliers : 2.16 % Allowed : 18.00 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.95 (0.13), residues: 4626 helix: 0.66 (0.12), residues: 1958 sheet: -1.86 (0.22), residues: 531 loop : -1.52 (0.14), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 292 HIS 0.015 0.001 HIS B 407 PHE 0.019 0.001 PHE C 466 TYR 0.023 0.002 TYR A 493 ARG 0.013 0.000 ARG C 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 310 time to evaluate : 4.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6401 (tpt) cc_final: 0.5521 (mpp) REVERT: A 698 MET cc_start: 0.2277 (mmt) cc_final: 0.1675 (mmt) REVERT: A 702 MET cc_start: 0.4586 (mtt) cc_final: 0.4315 (mtt) REVERT: A 713 MET cc_start: 0.6747 (tmm) cc_final: 0.5900 (tmm) REVERT: A 723 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6513 (mt) REVERT: C 230 MET cc_start: 0.5423 (mpp) cc_final: 0.5091 (mpp) REVERT: C 735 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7733 (mp) REVERT: E 273 LEU cc_start: 0.8098 (mt) cc_final: 0.7880 (mt) REVERT: E 543 LEU cc_start: 0.8094 (mt) cc_final: 0.7771 (tt) REVERT: E 563 TRP cc_start: 0.5548 (p90) cc_final: 0.4675 (p90) REVERT: E 620 SER cc_start: 0.7837 (m) cc_final: 0.7497 (t) REVERT: D 228 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8263 (tm-30) REVERT: D 251 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8187 (pttm) REVERT: D 401 MET cc_start: 0.6344 (tpp) cc_final: 0.5758 (tpp) REVERT: D 427 MET cc_start: 0.8135 (mtp) cc_final: 0.7863 (mtp) REVERT: D 698 MET cc_start: 0.3659 (mmm) cc_final: 0.3375 (mmt) REVERT: F 75 MET cc_start: 0.4370 (tmm) cc_final: 0.4106 (tmm) REVERT: B 85 MET cc_start: 0.0563 (mmt) cc_final: 0.0134 (tmm) REVERT: B 386 ASP cc_start: 0.8657 (p0) cc_final: 0.7870 (p0) REVERT: B 475 GLN cc_start: 0.7020 (mp10) cc_final: 0.6625 (mt0) outliers start: 84 outliers final: 73 residues processed: 368 average time/residue: 0.4575 time to fit residues: 284.4682 Evaluate side-chains 378 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 303 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 762 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 439 MET Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 558 TRP Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 4.9990 chunk 390 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 337 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 367 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 376 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 67 optimal weight: 40.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 666 HIS F 510 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.184840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.138902 restraints weight = 90504.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.130999 restraints weight = 78038.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.132774 restraints weight = 68578.580| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37249 Z= 0.176 Angle : 0.644 12.966 50505 Z= 0.306 Chirality : 0.043 0.213 5744 Planarity : 0.004 0.068 6557 Dihedral : 8.064 175.586 5161 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.77 % Favored : 94.21 % Rotamer: Outliers : 2.00 % Allowed : 18.44 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.83 (0.13), residues: 4626 helix: 0.77 (0.12), residues: 1960 sheet: -1.79 (0.22), residues: 526 loop : -1.45 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 431 HIS 0.010 0.001 HIS E 666 PHE 0.016 0.001 PHE F 657 TYR 0.021 0.001 TYR F 63 ARG 0.013 0.000 ARG C 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7453.56 seconds wall clock time: 137 minutes 3.43 seconds (8223.43 seconds total)