Starting phenix.real_space_refine on Fri Mar 15 20:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/03_2024/7dd6_30645.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 70 5.16 5 Cl 2 4.86 5 C 8213 2.51 5 N 2028 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 216": "OD1" <-> "OD2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A ASP 479": "OD1" <-> "OD2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ASP 587": "OD1" <-> "OD2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 575": "OE1" <-> "OE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B GLU 603": "OE1" <-> "OE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12678 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6209 Classifications: {'peptide': 791} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6235 Classifications: {'peptide': 792} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.08, per 1000 atoms: 0.56 Number of scatterers: 12678 At special positions: 0 Unit cell: (100.386, 93.288, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 Cl 2 17.00 S 70 16.00 O 2359 8.00 N 2028 7.00 C 8213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.73 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.24 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.49 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.66 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=1.82 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 764 " distance=2.39 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 399 " " NAG A1107 " - " ASN A 467 " " NAG B1105 " - " ASN B 287 " " NAG B1106 " - " ASN B 399 " " NAG B1107 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 49.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.641A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.712A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.707A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.561A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.387A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.780A pdb=" N VAL A 403 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.594A pdb=" N LYS A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 454 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.526A pdb=" N HIS A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 609 through 636 Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.209A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.557A pdb=" N ILE A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 697 removed outlier: 3.577A pdb=" N CYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 720 through 745 removed outlier: 3.605A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 792 Processing helix chain 'A' and resid 801 through 826 removed outlier: 4.163A pdb=" N PHE A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Proline residue: A 822 - end of helix removed outlier: 3.552A pdb=" N SER A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 862 removed outlier: 3.798A pdb=" N SER A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.728A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.027A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.643A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.530A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.913A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.501A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.703A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.733A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.621A pdb=" N LYS B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 454' Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.617A pdb=" N HIS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 636 Processing helix chain 'B' and resid 639 through 644 removed outlier: 4.097A pdb=" N LYS B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.626A pdb=" N ILE B 668 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 697 Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 720 through 743 removed outlier: 4.080A pdb=" N PHE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 793 removed outlier: 3.603A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.978A pdb=" N PHE B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 828 through 862 removed outlier: 3.615A pdb=" N SER B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.103A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.819A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.983A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 488 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS A 509 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 490 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'A' and resid 601 through 603 removed outlier: 6.751A pdb=" N GLN A 601 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE A 762 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 603 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N CYS A 764 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.971A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.849A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.919A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 317 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 488 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS B 509 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 490 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB4, first strand: chain 'B' and resid 549 through 552 Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AB6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 603 removed outlier: 4.117A pdb=" N ILE B 762 " --> pdb=" O GLU B 603 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1722 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: 3.99 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2054 1.31 - 1.44: 3635 1.44 - 1.57: 7216 1.57 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 12991 Sorted by residual: bond pdb=" C7 NAG A1107 " pdb=" N2 NAG A1107 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C7 NAG B1105 " pdb=" N2 NAG B1105 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C7 NAG B1106 " pdb=" N2 NAG B1106 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG B1107 " pdb=" N2 NAG B1107 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.73: 377 106.73 - 113.62: 7115 113.62 - 120.52: 5354 120.52 - 127.42: 4653 127.42 - 134.32: 142 Bond angle restraints: 17641 Sorted by residual: angle pdb=" C THR B 698 " pdb=" N ASN B 699 " pdb=" CA ASN B 699 " ideal model delta sigma weight residual 120.71 127.74 -7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" C ILE B 740 " pdb=" N TRP B 741 " pdb=" CA TRP B 741 " ideal model delta sigma weight residual 120.28 114.96 5.32 1.34e+00 5.57e-01 1.58e+01 angle pdb=" CA ARG B 700 " pdb=" C ARG B 700 " pdb=" O ARG B 700 " ideal model delta sigma weight residual 122.44 117.38 5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" CA ARG A 700 " pdb=" C ARG A 700 " pdb=" O ARG A 700 " ideal model delta sigma weight residual 122.44 117.39 5.05 1.34e+00 5.57e-01 1.42e+01 angle pdb=" N LYS A 697 " pdb=" CA LYS A 697 " pdb=" C LYS A 697 " ideal model delta sigma weight residual 113.21 109.06 4.15 1.15e+00 7.56e-01 1.30e+01 ... (remaining 17636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 7193 23.36 - 46.72: 510 46.72 - 70.08: 89 70.08 - 93.44: 30 93.44 - 116.80: 7 Dihedral angle restraints: 7829 sinusoidal: 3225 harmonic: 4604 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 676 " pdb=" SG CYS B 676 " pdb=" SG CYS B 764 " pdb=" CB CYS B 764 " ideal model delta sinusoidal sigma weight residual 93.00 7.40 85.60 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual 93.00 16.54 76.46 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 7826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1921 0.105 - 0.210: 80 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 2005 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.78e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA VAL A 704 " pdb=" N VAL A 704 " pdb=" C VAL A 704 " pdb=" CB VAL A 704 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2002 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 697 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C LYS B 697 " -0.082 2.00e-02 2.50e+03 pdb=" O LYS B 697 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 698 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 670 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 671 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 671 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 671 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 188 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 374 2.68 - 3.24: 13018 3.24 - 3.79: 19599 3.79 - 4.35: 25818 4.35 - 4.90: 42025 Nonbonded interactions: 100834 Sorted by model distance: nonbonded pdb=" O LEU B 430 " pdb=" CG2 ILE B 433 " model vdw 2.126 3.460 nonbonded pdb=" O ILE B 623 " pdb=" OG1 THR B 626 " model vdw 2.147 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O TRP B1108 " model vdw 2.153 2.440 nonbonded pdb=" O ALA A 110 " pdb=" OG SER A 113 " model vdw 2.187 2.440 nonbonded pdb=" OG SER B 150 " pdb=" OG SER B 169 " model vdw 2.192 2.440 ... (remaining 100829 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 22 through 119 or resid 136 through 867 or resid 1101 thro \ ugh 1108)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 867 or \ resid 1101 through 1108)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.320 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.380 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.008 0.107 12991 Z= 0.526 Angle : 0.809 10.169 17641 Z= 0.451 Chirality : 0.050 0.525 2005 Planarity : 0.004 0.051 2229 Dihedral : 16.894 116.801 4798 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.07 % Allowed : 20.34 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.18), residues: 1567 helix: -1.20 (0.17), residues: 685 sheet: -2.17 (0.37), residues: 153 loop : -2.84 (0.18), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 765 PHE 0.015 0.001 PHE B 562 TYR 0.014 0.001 TYR A 750 ARG 0.004 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9125 (tp) cc_final: 0.8882 (tt) REVERT: A 571 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 587 ASP cc_start: 0.8364 (p0) cc_final: 0.7842 (t0) REVERT: A 756 GLU cc_start: 0.7753 (tp30) cc_final: 0.7148 (tp30) REVERT: A 810 MET cc_start: 0.6302 (mtm) cc_final: 0.5673 (mtm) REVERT: A 813 PHE cc_start: 0.6804 (t80) cc_final: 0.6536 (t80) REVERT: B 472 MET cc_start: 0.8335 (mtm) cc_final: 0.8129 (mtm) REVERT: B 752 ASN cc_start: 0.8592 (t0) cc_final: 0.8192 (m110) REVERT: B 787 PHE cc_start: 0.7982 (t80) cc_final: 0.7728 (t80) REVERT: B 800 PHE cc_start: 0.8809 (m-10) cc_final: 0.8290 (m-80) REVERT: B 805 PHE cc_start: 0.8393 (m-80) cc_final: 0.7817 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2615 time to fit residues: 73.0870 Evaluate side-chains 105 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 741 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 335 GLN A 465 HIS A 672 GLN A 734 GLN A 752 ASN A 799 ASN B 23 ASN B 118 ASN B 193 GLN B 245 GLN B 260 GLN B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS B 494 HIS B 509 HIS B 734 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12991 Z= 0.247 Angle : 0.667 11.413 17641 Z= 0.334 Chirality : 0.050 0.728 2005 Planarity : 0.005 0.062 2229 Dihedral : 9.489 110.315 1975 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.64 % Allowed : 20.79 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.20), residues: 1567 helix: 0.14 (0.19), residues: 707 sheet: -1.62 (0.37), residues: 177 loop : -2.28 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 674 HIS 0.004 0.001 HIS A 594 PHE 0.041 0.002 PHE A 814 TYR 0.011 0.001 TYR A 417 ARG 0.008 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 114 time to evaluate : 1.627 Fit side-chains REVERT: A 528 LEU cc_start: 0.9084 (tp) cc_final: 0.8797 (tt) REVERT: A 587 ASP cc_start: 0.8344 (p0) cc_final: 0.7737 (t0) REVERT: A 641 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6126 (mt) REVERT: A 751 ARG cc_start: 0.7425 (ptm160) cc_final: 0.6582 (ptm160) REVERT: A 752 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8354 (t0) REVERT: A 756 GLU cc_start: 0.7724 (tp30) cc_final: 0.7170 (tp30) REVERT: A 791 PHE cc_start: 0.8796 (t80) cc_final: 0.8572 (p90) REVERT: A 810 MET cc_start: 0.6023 (mtm) cc_final: 0.5684 (mtm) REVERT: A 814 PHE cc_start: 0.8029 (m-80) cc_final: 0.7812 (m-80) REVERT: A 845 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: B 741 TRP cc_start: 0.5669 (t60) cc_final: 0.5357 (t60) REVERT: B 759 ILE cc_start: 0.6616 (mt) cc_final: 0.6213 (mm) REVERT: B 787 PHE cc_start: 0.8181 (t80) cc_final: 0.7886 (t80) outliers start: 49 outliers final: 21 residues processed: 151 average time/residue: 0.1962 time to fit residues: 47.0493 Evaluate side-chains 119 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12991 Z= 0.263 Angle : 0.624 10.417 17641 Z= 0.310 Chirality : 0.048 0.692 2005 Planarity : 0.004 0.064 2229 Dihedral : 8.051 110.156 1973 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.56 % Allowed : 21.38 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1567 helix: 0.63 (0.19), residues: 701 sheet: -1.39 (0.38), residues: 180 loop : -2.05 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 299 HIS 0.003 0.001 HIS A 753 PHE 0.036 0.002 PHE A 724 TYR 0.011 0.001 TYR A 417 ARG 0.004 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 101 time to evaluate : 1.332 Fit side-chains REVERT: A 587 ASP cc_start: 0.8351 (p0) cc_final: 0.7727 (t0) REVERT: A 641 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6558 (tt) REVERT: A 756 GLU cc_start: 0.7809 (tp30) cc_final: 0.7267 (tp30) REVERT: A 810 MET cc_start: 0.6064 (mtm) cc_final: 0.5677 (mtm) REVERT: A 814 PHE cc_start: 0.8024 (m-80) cc_final: 0.7704 (m-80) REVERT: A 845 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 725 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 741 TRP cc_start: 0.5912 (t60) cc_final: 0.5522 (t60) outliers start: 48 outliers final: 24 residues processed: 139 average time/residue: 0.1807 time to fit residues: 40.3870 Evaluate side-chains 119 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.8980 chunk 108 optimal weight: 0.0870 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 752 ASN B 338 HIS ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12991 Z= 0.156 Angle : 0.578 14.288 17641 Z= 0.279 Chirality : 0.047 0.681 2005 Planarity : 0.004 0.066 2229 Dihedral : 7.467 108.467 1973 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.41 % Allowed : 22.64 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1567 helix: 0.92 (0.19), residues: 712 sheet: -1.21 (0.38), residues: 188 loop : -1.72 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 299 HIS 0.003 0.001 HIS A 594 PHE 0.026 0.001 PHE A 724 TYR 0.012 0.001 TYR A 824 ARG 0.004 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.517 Fit side-chains REVERT: A 413 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7599 (mp) REVERT: A 587 ASP cc_start: 0.8330 (p0) cc_final: 0.7682 (t0) REVERT: A 641 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6684 (tt) REVERT: A 741 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.7147 (m100) REVERT: A 752 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.6898 (p0) REVERT: A 756 GLU cc_start: 0.7675 (tp30) cc_final: 0.7161 (tp30) REVERT: A 772 LEU cc_start: 0.8966 (pp) cc_final: 0.8736 (pp) REVERT: A 808 PHE cc_start: 0.8198 (m-80) cc_final: 0.7986 (m-80) REVERT: A 845 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: B 307 MET cc_start: 0.7691 (mtp) cc_final: 0.7069 (mtt) REVERT: B 462 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.8042 (m-70) REVERT: B 698 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7751 (p) REVERT: B 741 TRP cc_start: 0.5816 (t60) cc_final: 0.5448 (t-100) REVERT: B 751 ARG cc_start: 0.9256 (mtp85) cc_final: 0.9030 (mtp85) outliers start: 46 outliers final: 22 residues processed: 139 average time/residue: 0.1884 time to fit residues: 42.0235 Evaluate side-chains 124 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 0.0040 chunk 63 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 12991 Z= 0.432 Angle : 0.685 15.232 17641 Z= 0.342 Chirality : 0.051 0.706 2005 Planarity : 0.005 0.069 2229 Dihedral : 7.679 109.714 1973 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.05 % Allowed : 22.27 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1567 helix: 0.96 (0.19), residues: 707 sheet: -1.26 (0.37), residues: 199 loop : -1.80 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1108 HIS 0.005 0.001 HIS B 753 PHE 0.018 0.002 PHE A 724 TYR 0.012 0.002 TYR B 203 ARG 0.004 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 92 time to evaluate : 1.456 Fit side-chains REVERT: A 587 ASP cc_start: 0.8435 (p0) cc_final: 0.7664 (t0) REVERT: A 756 GLU cc_start: 0.7833 (tp30) cc_final: 0.7284 (tp30) REVERT: A 810 MET cc_start: 0.6181 (mtm) cc_final: 0.5551 (mtt) REVERT: A 814 PHE cc_start: 0.8060 (m-80) cc_final: 0.7661 (m-80) REVERT: A 845 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: B 692 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7793 (p) REVERT: B 698 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7700 (p) REVERT: B 721 ASN cc_start: 0.1938 (OUTLIER) cc_final: 0.1414 (m-40) REVERT: B 725 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8011 (mt) outliers start: 68 outliers final: 43 residues processed: 148 average time/residue: 0.1802 time to fit residues: 42.8992 Evaluate side-chains 135 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 87 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12991 Z= 0.300 Angle : 0.628 16.241 17641 Z= 0.307 Chirality : 0.048 0.708 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.603 109.784 1973 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.31 % Allowed : 22.64 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1567 helix: 1.11 (0.19), residues: 704 sheet: -1.36 (0.36), residues: 215 loop : -1.64 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.003 0.001 HIS B 494 PHE 0.021 0.001 PHE A 774 TYR 0.011 0.001 TYR B 203 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 1.494 Fit side-chains REVERT: A 528 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 587 ASP cc_start: 0.8508 (p0) cc_final: 0.7789 (t0) REVERT: A 756 GLU cc_start: 0.7883 (tp30) cc_final: 0.7321 (tp30) REVERT: A 787 PHE cc_start: 0.8098 (t80) cc_final: 0.7853 (t80) REVERT: A 810 MET cc_start: 0.6251 (mtm) cc_final: 0.5515 (mtm) REVERT: A 814 PHE cc_start: 0.8041 (m-80) cc_final: 0.7631 (m-80) REVERT: A 845 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: B 307 MET cc_start: 0.7793 (mtp) cc_final: 0.7261 (mtt) REVERT: B 698 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7705 (p) REVERT: B 721 ASN cc_start: 0.1617 (OUTLIER) cc_final: 0.1101 (m-40) REVERT: B 725 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7970 (mt) outliers start: 58 outliers final: 44 residues processed: 138 average time/residue: 0.1925 time to fit residues: 42.3148 Evaluate side-chains 134 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 85 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12991 Z= 0.165 Angle : 0.598 16.002 17641 Z= 0.287 Chirality : 0.047 0.688 2005 Planarity : 0.004 0.071 2229 Dihedral : 7.386 108.419 1973 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.64 % Allowed : 23.90 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1567 helix: 1.27 (0.20), residues: 703 sheet: -1.07 (0.38), residues: 198 loop : -1.56 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 299 HIS 0.003 0.001 HIS A 594 PHE 0.025 0.001 PHE A 774 TYR 0.010 0.001 TYR A 824 ARG 0.005 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 89 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 587 ASP cc_start: 0.8488 (p0) cc_final: 0.7818 (t0) REVERT: A 751 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7799 (mtp180) REVERT: A 756 GLU cc_start: 0.7871 (tp30) cc_final: 0.7281 (tp30) REVERT: A 787 PHE cc_start: 0.8147 (t80) cc_final: 0.7861 (t80) REVERT: A 810 MET cc_start: 0.6261 (mtm) cc_final: 0.5568 (mtm) REVERT: A 814 PHE cc_start: 0.8082 (m-80) cc_final: 0.7645 (m-80) REVERT: A 845 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: B 307 MET cc_start: 0.7743 (mtp) cc_final: 0.7209 (mtt) REVERT: B 571 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: B 698 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7787 (p) REVERT: B 721 ASN cc_start: 0.1485 (OUTLIER) cc_final: 0.0998 (m-40) REVERT: B 725 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7982 (mt) outliers start: 49 outliers final: 36 residues processed: 129 average time/residue: 0.1856 time to fit residues: 39.0966 Evaluate side-chains 130 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 88 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 335 GLN A 594 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12991 Z= 0.203 Angle : 0.593 16.579 17641 Z= 0.286 Chirality : 0.047 0.678 2005 Planarity : 0.004 0.074 2229 Dihedral : 7.308 107.995 1973 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.34 % Allowed : 24.57 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1567 helix: 1.34 (0.20), residues: 704 sheet: -1.10 (0.39), residues: 190 loop : -1.47 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.003 0.001 HIS A 594 PHE 0.030 0.001 PHE A 774 TYR 0.012 0.001 TYR A 824 ARG 0.003 0.000 ARG B 751 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 587 ASP cc_start: 0.8496 (p0) cc_final: 0.7780 (t0) REVERT: A 751 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7724 (mtp180) REVERT: A 756 GLU cc_start: 0.7850 (tp30) cc_final: 0.7173 (tp30) REVERT: A 787 PHE cc_start: 0.8152 (t80) cc_final: 0.7859 (t80) REVERT: A 810 MET cc_start: 0.6269 (mtm) cc_final: 0.5536 (mtt) REVERT: A 814 PHE cc_start: 0.8071 (m-80) cc_final: 0.7627 (m-80) REVERT: B 571 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 698 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7790 (p) REVERT: B 721 ASN cc_start: 0.1533 (OUTLIER) cc_final: 0.0947 (m-40) REVERT: B 725 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7966 (mt) outliers start: 45 outliers final: 33 residues processed: 128 average time/residue: 0.1747 time to fit residues: 36.1537 Evaluate side-chains 126 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 128 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 93 optimal weight: 0.0370 chunk 150 optimal weight: 20.0000 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12991 Z= 0.250 Angle : 0.615 17.069 17641 Z= 0.297 Chirality : 0.048 0.685 2005 Planarity : 0.004 0.071 2229 Dihedral : 7.361 108.254 1973 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.34 % Allowed : 24.72 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1567 helix: 1.38 (0.20), residues: 704 sheet: -0.99 (0.38), residues: 199 loop : -1.44 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.003 0.001 HIS B 753 PHE 0.033 0.001 PHE A 774 TYR 0.011 0.001 TYR A 824 ARG 0.002 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 88 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 587 ASP cc_start: 0.8558 (p0) cc_final: 0.7744 (t0) REVERT: A 751 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7713 (mtp180) REVERT: A 756 GLU cc_start: 0.7871 (tp30) cc_final: 0.7040 (tp30) REVERT: A 787 PHE cc_start: 0.8166 (t80) cc_final: 0.7868 (t80) REVERT: A 810 MET cc_start: 0.6311 (mtm) cc_final: 0.5601 (mtm) REVERT: A 814 PHE cc_start: 0.8032 (m-80) cc_final: 0.7591 (m-80) REVERT: B 571 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 721 ASN cc_start: 0.1526 (OUTLIER) cc_final: 0.0911 (m-40) REVERT: B 725 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8075 (mt) outliers start: 45 outliers final: 36 residues processed: 127 average time/residue: 0.1987 time to fit residues: 40.3736 Evaluate side-chains 128 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 0.2980 chunk 144 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12991 Z= 0.286 Angle : 0.627 17.211 17641 Z= 0.306 Chirality : 0.048 0.693 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.504 108.920 1973 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.64 % Allowed : 24.42 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1567 helix: 1.41 (0.20), residues: 702 sheet: -0.93 (0.40), residues: 187 loop : -1.45 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 674 HIS 0.003 0.001 HIS B 753 PHE 0.035 0.001 PHE A 774 TYR 0.011 0.001 TYR B 824 ARG 0.002 0.000 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 751 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: A 756 GLU cc_start: 0.7829 (tp30) cc_final: 0.7000 (tp30) REVERT: A 787 PHE cc_start: 0.8153 (t80) cc_final: 0.7875 (t80) REVERT: A 808 PHE cc_start: 0.8298 (m-80) cc_final: 0.7809 (m-80) REVERT: A 810 MET cc_start: 0.6335 (mtm) cc_final: 0.5647 (mtm) REVERT: A 814 PHE cc_start: 0.8029 (m-80) cc_final: 0.7612 (m-80) REVERT: A 845 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: B 571 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 698 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7830 (p) REVERT: B 721 ASN cc_start: 0.1341 (OUTLIER) cc_final: 0.0686 (m-40) REVERT: B 725 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (mt) outliers start: 49 outliers final: 39 residues processed: 130 average time/residue: 0.1877 time to fit residues: 39.7463 Evaluate side-chains 132 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 86 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.125022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083660 restraints weight = 26769.836| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.96 r_work: 0.3177 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12991 Z= 0.164 Angle : 0.592 17.050 17641 Z= 0.282 Chirality : 0.046 0.665 2005 Planarity : 0.004 0.068 2229 Dihedral : 7.243 107.128 1973 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.97 % Allowed : 25.02 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.21), residues: 1567 helix: 1.49 (0.20), residues: 703 sheet: -0.88 (0.42), residues: 170 loop : -1.23 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 299 HIS 0.002 0.000 HIS A 462 PHE 0.033 0.001 PHE A 774 TYR 0.012 0.001 TYR B 824 ARG 0.002 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.67 seconds wall clock time: 46 minutes 10.74 seconds (2770.74 seconds total)