Starting phenix.real_space_refine on Fri Jan 19 20:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7neq_12290/01_2024/7neq_12290_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 68 5.16 5 C 8112 2.51 5 N 2039 2.21 5 O 2309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 620": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 2, 'NAG': 1, 'U9N': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'CLR': 1, 'NAG': 1, 'R1H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 7.43, per 1000 atoms: 0.59 Number of scatterers: 12529 At special positions: 0 Unit cell: (102.3, 97.02, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 1 15.00 O 2309 8.00 N 2039 7.00 C 8112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.82 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 596 " " NAG B1102 " - " ASN B 596 " Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.3 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 13 sheets defined 39.3% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.831A pdb=" N LEU A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASP A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 4.464A pdb=" N LYS A 118 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 119 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.841A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 220 through 234 removed outlier: 4.587A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.601A pdb=" N LYS A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 329 through 338 removed outlier: 3.677A pdb=" N ALA A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 4.088A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.855A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 412 Processing helix chain 'A' and resid 420 through 449 removed outlier: 4.353A pdb=" N GLN A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.818A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.977A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.413A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 571' Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.802A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.869A pdb=" N LEU B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.968A pdb=" N LYS B 118 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.592A pdb=" N LEU B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 removed outlier: 3.537A pdb=" N GLU B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 199 removed outlier: 4.007A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.718A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.641A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 329 through 338 removed outlier: 4.005A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 removed outlier: 4.673A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 removed outlier: 4.190A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 412 Processing helix chain 'B' and resid 420 through 445 removed outlier: 4.439A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 472 Processing helix chain 'B' and resid 484 through 496 removed outlier: 3.937A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.801A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 552 removed outlier: 4.035A pdb=" N LEU B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 570 removed outlier: 4.305A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 570' Processing helix chain 'B' and resid 573 through 586 Processing helix chain 'B' and resid 610 through 616 Processing helix chain 'B' and resid 623 through 649 removed outlier: 5.072A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN B 629 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA B 632 " --> pdb=" O ASN B 629 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 39 removed outlier: 3.749A pdb=" N LEU A 37 " --> pdb=" O MET A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 269 removed outlier: 6.321A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU A 75 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR A 257 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 77 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 259 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 79 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 19 through 24 removed outlier: 4.103A pdb=" N TYR C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 33 through 38 Processing sheet with id= E, first strand: chain 'D' and resid 6 through 8 Processing sheet with id= F, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.823A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.999A pdb=" N LYS E 103 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N VAL E 13 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU E 105 " --> pdb=" O VAL E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.536A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 85 through 90 removed outlier: 6.129A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 3 through 8 Processing sheet with id= K, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.655A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.799A pdb=" N LEU B 37 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 69 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.265A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N THR B 257 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ALA B 77 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LEU B 259 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 79 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1260 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: 3.80 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1940 1.26 - 1.40: 3242 1.40 - 1.54: 7446 1.54 - 1.68: 66 1.68 - 1.83: 106 Bond restraints: 12800 Sorted by residual: bond pdb=" C13 R1H B1101 " pdb=" N08 R1H B1101 " ideal model delta sigma weight residual 1.455 1.148 0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C03 R1H B1101 " pdb=" C04 R1H B1101 " ideal model delta sigma weight residual 1.396 1.113 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C10 R1H B1101 " pdb=" C11 R1H B1101 " ideal model delta sigma weight residual 1.534 1.254 0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C04 R1H B1101 " pdb=" C05 R1H B1101 " ideal model delta sigma weight residual 1.392 1.249 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C11 R1H B1101 " pdb=" C12 R1H B1101 " ideal model delta sigma weight residual 1.400 1.527 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 12795 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.63: 315 106.63 - 113.57: 7119 113.57 - 120.51: 5066 120.51 - 127.44: 4741 127.44 - 134.38: 114 Bond angle restraints: 17355 Sorted by residual: angle pdb=" N TYR F 95 " pdb=" CA TYR F 95 " pdb=" C TYR F 95 " ideal model delta sigma weight residual 110.80 123.94 -13.14 2.13e+00 2.20e-01 3.80e+01 angle pdb=" N ASN F 36 " pdb=" CA ASN F 36 " pdb=" C ASN F 36 " ideal model delta sigma weight residual 109.81 117.52 -7.71 1.53e+00 4.27e-01 2.54e+01 angle pdb=" N CYS D 96 " pdb=" CA CYS D 96 " pdb=" C CYS D 96 " ideal model delta sigma weight residual 109.59 101.62 7.97 1.61e+00 3.86e-01 2.45e+01 angle pdb=" C10 R1H B1101 " pdb=" C11 R1H B1101 " pdb=" C12 R1H B1101 " ideal model delta sigma weight residual 121.26 134.38 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" N TYR F 94 " pdb=" CA TYR F 94 " pdb=" C TYR F 94 " ideal model delta sigma weight residual 113.88 119.15 -5.27 1.23e+00 6.61e-01 1.84e+01 ... (remaining 17350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6609 17.87 - 35.74: 817 35.74 - 53.60: 204 53.60 - 71.47: 48 71.47 - 89.34: 15 Dihedral angle restraints: 7693 sinusoidal: 3157 harmonic: 4536 Sorted by residual: dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual 93.00 25.18 67.82 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 41.27 51.73 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA ASP D 32 " pdb=" C ASP D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1853 0.088 - 0.175: 114 0.175 - 0.263: 6 0.263 - 0.351: 4 0.351 - 0.438: 2 Chirality restraints: 1979 Sorted by residual: chirality pdb=" CA TYR F 95 " pdb=" N TYR F 95 " pdb=" C TYR F 95 " pdb=" CB TYR F 95 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA TYR F 94 " pdb=" N TYR F 94 " pdb=" C TYR F 94 " pdb=" CB TYR F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C2 U9N A1002 " pdb=" C1 U9N A1002 " pdb=" C3 U9N A1002 " pdb=" O2 U9N A1002 " both_signs ideal model delta sigma weight residual False 2.24 2.53 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1976 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 87 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 88 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 95 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C TYR D 95 " -0.036 2.00e-02 2.50e+03 pdb=" O TYR D 95 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS D 96 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO F 88 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.029 5.00e-02 4.00e+02 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 16 2.26 - 2.92: 5410 2.92 - 3.58: 17301 3.58 - 4.24: 28509 4.24 - 4.90: 49763 Nonbonded interactions: 100999 Sorted by model distance: nonbonded pdb=" OD1 ASP B 217 " pdb=" CG2 THR B 220 " model vdw 1.600 3.460 nonbonded pdb=" OD1 ASN B 76 " pdb=" N SER B 255 " model vdw 1.732 2.520 nonbonded pdb=" CE1 TYR B 464 " pdb=" CB TYR B 469 " model vdw 2.051 3.740 nonbonded pdb=" NH1 ARG C 45 " pdb=" CE2 PHE C 58 " model vdw 2.058 3.420 nonbonded pdb=" NH1 ARG C 45 " pdb=" CZ PHE C 58 " model vdw 2.070 3.420 ... (remaining 100994 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 35 through 654 or resid 1003)) selection = (chain 'B' and (resid 35 through 654 or resid 1103)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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: 2.800 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: 12.800 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.040 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.307 12800 Z= 0.434 Angle : 0.792 13.138 17355 Z= 0.398 Chirality : 0.049 0.438 1979 Planarity : 0.004 0.056 2142 Dihedral : 16.913 89.340 4776 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.56 % Allowed : 22.89 % Favored : 71.56 % 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: -3.70 (0.18), residues: 1558 helix: -1.59 (0.18), residues: 652 sheet: -1.97 (0.28), residues: 286 loop : -3.59 (0.20), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 PHE 0.024 0.002 PHE F 79 TYR 0.016 0.002 TYR A 123 ARG 0.004 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 218 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.6881 (t0) cc_final: 0.6678 (t0) REVERT: A 190 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5260 (mm-30) REVERT: A 234 GLN cc_start: 0.6354 (mm-40) cc_final: 0.5977 (mp10) REVERT: A 278 GLU cc_start: 0.4383 (OUTLIER) cc_final: 0.4181 (mt-10) REVERT: A 334 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.5014 (mm-30) REVERT: A 458 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6487 (mm-30) REVERT: A 463 TYR cc_start: 0.7804 (m-80) cc_final: 0.7536 (m-80) REVERT: D 16 GLN cc_start: 0.7250 (tt0) cc_final: 0.6919 (tp40) REVERT: D 18 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7241 (tp) REVERT: E 82 ASP cc_start: 0.7201 (m-30) cc_final: 0.6954 (m-30) REVERT: E 107 ARG cc_start: 0.4954 (mtt90) cc_final: 0.4745 (mmp-170) REVERT: B 66 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6325 (t0) REVERT: B 98 ASP cc_start: 0.6365 (t0) cc_final: 0.5954 (p0) outliers start: 75 outliers final: 54 residues processed: 279 average time/residue: 0.2625 time to fit residues: 103.4486 Evaluate side-chains 227 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 169 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 587 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 ASN A 66 ASN A 109 ASN A 299 ASN A 375 HIS A 398 GLN A 425 ASN A 436 ASN A 531 GLN A 583 HIS A 590 ASN D 36 ASN E 31 ASN E 37 GLN F 36 ASN B 40 HIS B 68 ASN B 243 HIS B 283 HIS B 425 ASN B 436 ASN B 531 GLN B 582 GLN B 583 HIS B 601 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12800 Z= 0.249 Angle : 0.627 10.396 17355 Z= 0.314 Chirality : 0.042 0.160 1979 Planarity : 0.004 0.055 2142 Dihedral : 9.720 79.140 2077 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.48 % Allowed : 25.63 % Favored : 68.89 % 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: -2.45 (0.20), residues: 1558 helix: -0.45 (0.20), residues: 652 sheet: -1.45 (0.29), residues: 286 loop : -2.98 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 PHE 0.030 0.002 PHE B 250 TYR 0.012 0.001 TYR C 91 ARG 0.006 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 182 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 VAL cc_start: 0.6565 (p) cc_final: 0.6069 (p) REVERT: A 226 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6665 (mm) REVERT: A 234 GLN cc_start: 0.6475 (mm-40) cc_final: 0.5959 (mp10) REVERT: A 458 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 463 TYR cc_start: 0.7889 (m-80) cc_final: 0.7489 (m-80) REVERT: A 510 MET cc_start: 0.7038 (ttp) cc_final: 0.6796 (ttp) REVERT: A 587 LEU cc_start: 0.7444 (mt) cc_final: 0.6982 (mt) REVERT: D 16 GLN cc_start: 0.7256 (tt0) cc_final: 0.6913 (tp40) REVERT: D 65 ARG cc_start: 0.7140 (tpm170) cc_final: 0.6828 (mmp80) REVERT: E 107 ARG cc_start: 0.4931 (mtt90) cc_final: 0.4722 (mmp-170) REVERT: B 64 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6523 (mp) REVERT: B 66 ASN cc_start: 0.6643 (t0) cc_final: 0.6372 (t0) REVERT: B 272 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6903 (mp0) outliers start: 74 outliers final: 49 residues processed: 244 average time/residue: 0.2365 time to fit residues: 85.1264 Evaluate side-chains 222 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 95 optimal weight: 0.0170 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 0.0170 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN D 5 GLN B 40 HIS B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12800 Z= 0.222 Angle : 0.588 9.129 17355 Z= 0.296 Chirality : 0.041 0.164 1979 Planarity : 0.004 0.053 2142 Dihedral : 8.026 75.048 2006 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.59 % Allowed : 25.19 % Favored : 68.22 % 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: -1.86 (0.21), residues: 1558 helix: 0.01 (0.20), residues: 650 sheet: -1.14 (0.30), residues: 286 loop : -2.63 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 PHE 0.027 0.001 PHE B 250 TYR 0.022 0.001 TYR B 342 ARG 0.004 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 176 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6620 (mm) REVERT: A 234 GLN cc_start: 0.6498 (mm-40) cc_final: 0.5980 (mp10) REVERT: A 278 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.3918 (mt-10) REVERT: A 458 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6432 (mm-30) REVERT: D 6 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: D 16 GLN cc_start: 0.7247 (tt0) cc_final: 0.6925 (tp40) REVERT: D 65 ARG cc_start: 0.7098 (tpm170) cc_final: 0.6803 (mmp80) REVERT: E 82 ASP cc_start: 0.7243 (m-30) cc_final: 0.7038 (m-30) REVERT: E 107 ARG cc_start: 0.4925 (mtt90) cc_final: 0.4723 (mmp-170) REVERT: B 64 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6599 (mp) REVERT: B 66 ASN cc_start: 0.6697 (t0) cc_final: 0.6457 (t0) REVERT: B 98 ASP cc_start: 0.6334 (t0) cc_final: 0.5912 (p0) REVERT: B 272 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6876 (mp0) outliers start: 89 outliers final: 65 residues processed: 245 average time/residue: 0.2429 time to fit residues: 86.7082 Evaluate side-chains 242 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 172 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 66 ASN A 375 HIS A 457 HIS F 36 ASN B 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12800 Z= 0.312 Angle : 0.634 10.069 17355 Z= 0.320 Chirality : 0.043 0.195 1979 Planarity : 0.004 0.053 2142 Dihedral : 8.022 82.240 2002 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 7.63 % Allowed : 25.11 % Favored : 67.26 % 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: -1.70 (0.21), residues: 1558 helix: 0.09 (0.20), residues: 652 sheet: -0.96 (0.31), residues: 286 loop : -2.54 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.004 0.001 HIS B 630 PHE 0.023 0.002 PHE B 250 TYR 0.018 0.002 TYR A 463 ARG 0.003 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 170 time to evaluate : 1.520 Fit side-chains REVERT: A 190 GLU cc_start: 0.5905 (mm-30) cc_final: 0.5040 (mm-30) REVERT: A 226 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6558 (mm) REVERT: A 234 GLN cc_start: 0.6524 (mm-40) cc_final: 0.5974 (mp10) REVERT: A 278 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3877 (mt-10) REVERT: A 343 LYS cc_start: 0.6894 (mmtt) cc_final: 0.6294 (mttm) REVERT: A 458 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6548 (mm-30) REVERT: C 11 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: D 5 GLN cc_start: 0.7323 (tm130) cc_final: 0.7122 (tt0) REVERT: D 16 GLN cc_start: 0.7269 (tt0) cc_final: 0.6962 (tp40) REVERT: D 18 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7161 (tp) REVERT: D 65 ARG cc_start: 0.7099 (tpm170) cc_final: 0.6814 (mmp80) REVERT: B 64 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6613 (mp) REVERT: B 207 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7273 (mp) REVERT: B 272 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6827 (mp0) outliers start: 103 outliers final: 85 residues processed: 253 average time/residue: 0.2154 time to fit residues: 80.2767 Evaluate side-chains 257 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 165 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 375 HIS D 5 GLN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12800 Z= 0.246 Angle : 0.592 9.306 17355 Z= 0.300 Chirality : 0.042 0.189 1979 Planarity : 0.004 0.052 2142 Dihedral : 7.688 79.290 2000 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.63 % Allowed : 24.81 % Favored : 67.56 % 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: -1.48 (0.21), residues: 1558 helix: 0.27 (0.21), residues: 652 sheet: -0.85 (0.31), residues: 286 loop : -2.41 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.003 0.001 HIS B 630 PHE 0.017 0.001 PHE F 79 TYR 0.014 0.001 TYR A 463 ARG 0.008 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 173 time to evaluate : 1.292 Fit side-chains REVERT: A 156 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: A 190 GLU cc_start: 0.5930 (mm-30) cc_final: 0.5116 (mm-30) REVERT: A 226 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6542 (mm) REVERT: A 234 GLN cc_start: 0.6534 (mm-40) cc_final: 0.5985 (mp10) REVERT: A 278 GLU cc_start: 0.4247 (OUTLIER) cc_final: 0.3902 (mt-10) REVERT: A 343 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6306 (mttm) REVERT: A 458 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6451 (mm-30) REVERT: C 11 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: D 16 GLN cc_start: 0.7245 (tt0) cc_final: 0.6964 (tp40) REVERT: D 18 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7169 (tp) REVERT: D 65 ARG cc_start: 0.7087 (tpm170) cc_final: 0.6827 (mmp80) REVERT: D 84 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7441 (ptt-90) REVERT: B 64 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6574 (mp) REVERT: B 66 ASN cc_start: 0.6652 (OUTLIER) cc_final: 0.6421 (t0) REVERT: B 272 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6865 (mp0) outliers start: 103 outliers final: 79 residues processed: 256 average time/residue: 0.2129 time to fit residues: 81.2179 Evaluate side-chains 251 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 164 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.4980 chunk 134 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 375 HIS F 36 ASN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12800 Z= 0.253 Angle : 0.592 9.328 17355 Z= 0.300 Chirality : 0.042 0.190 1979 Planarity : 0.004 0.052 2142 Dihedral : 7.509 80.960 1995 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 8.07 % Allowed : 24.59 % Favored : 67.33 % 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: -1.26 (0.21), residues: 1558 helix: 0.53 (0.21), residues: 638 sheet: -0.77 (0.31), residues: 286 loop : -2.32 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.003 0.001 HIS B 630 PHE 0.018 0.001 PHE F 79 TYR 0.018 0.001 TYR A 463 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 171 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6866 (mmmt) REVERT: A 190 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5131 (mm-30) REVERT: A 226 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6549 (mm) REVERT: A 234 GLN cc_start: 0.6542 (mm-40) cc_final: 0.5991 (mp10) REVERT: A 278 GLU cc_start: 0.4293 (OUTLIER) cc_final: 0.3940 (mt-10) REVERT: A 343 LYS cc_start: 0.6910 (mmtt) cc_final: 0.6320 (mttm) REVERT: C 11 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: D 6 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7337 (pt0) REVERT: D 16 GLN cc_start: 0.7234 (tt0) cc_final: 0.6972 (tp40) REVERT: D 18 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7121 (tp) REVERT: D 65 ARG cc_start: 0.7100 (tpm170) cc_final: 0.6852 (mmp80) REVERT: D 84 ARG cc_start: 0.7697 (ptp90) cc_final: 0.7448 (ptt-90) REVERT: B 64 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6591 (mp) REVERT: B 66 ASN cc_start: 0.6648 (OUTLIER) cc_final: 0.6429 (t0) REVERT: B 272 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6871 (mp0) outliers start: 109 outliers final: 86 residues processed: 258 average time/residue: 0.2288 time to fit residues: 87.4393 Evaluate side-chains 263 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 168 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 549 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 375 HIS F 36 ASN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12800 Z= 0.211 Angle : 0.571 8.654 17355 Z= 0.289 Chirality : 0.041 0.186 1979 Planarity : 0.004 0.040 2142 Dihedral : 7.333 79.128 1995 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.11 % Allowed : 26.07 % Favored : 66.81 % 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: -1.06 (0.21), residues: 1558 helix: 0.70 (0.21), residues: 636 sheet: -0.58 (0.31), residues: 278 loop : -2.24 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.003 0.001 HIS B 630 PHE 0.024 0.001 PHE A 385 TYR 0.019 0.001 TYR A 463 ARG 0.007 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 177 time to evaluate : 1.505 Fit side-chains REVERT: A 118 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6837 (mmmt) REVERT: A 190 GLU cc_start: 0.5988 (mm-30) cc_final: 0.5224 (mm-30) REVERT: A 226 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6535 (mm) REVERT: A 234 GLN cc_start: 0.6521 (mm-40) cc_final: 0.5975 (mp10) REVERT: A 278 GLU cc_start: 0.4289 (OUTLIER) cc_final: 0.3959 (mt-10) REVERT: A 343 LYS cc_start: 0.6867 (mmtt) cc_final: 0.6329 (mttm) REVERT: C 11 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: D 6 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7298 (pt0) REVERT: D 16 GLN cc_start: 0.7215 (tt0) cc_final: 0.6972 (tp40) REVERT: D 18 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7134 (tp) REVERT: D 65 ARG cc_start: 0.7080 (tpm170) cc_final: 0.6847 (mmp80) REVERT: D 84 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7449 (ptt-90) REVERT: B 64 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6526 (mp) REVERT: B 66 ASN cc_start: 0.6631 (OUTLIER) cc_final: 0.6430 (t0) REVERT: B 272 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7060 (mm-30) outliers start: 96 outliers final: 78 residues processed: 252 average time/residue: 0.2315 time to fit residues: 86.4671 Evaluate side-chains 257 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 170 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 651 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 158 ASN A 375 HIS F 36 ASN B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12800 Z= 0.367 Angle : 0.665 10.500 17355 Z= 0.336 Chirality : 0.045 0.198 1979 Planarity : 0.004 0.043 2142 Dihedral : 7.720 89.304 1995 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 7.78 % Allowed : 25.78 % Favored : 66.44 % 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: -1.28 (0.21), residues: 1558 helix: 0.46 (0.21), residues: 638 sheet: -0.63 (0.31), residues: 278 loop : -2.32 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 48 HIS 0.005 0.001 HIS B 630 PHE 0.020 0.002 PHE F 99 TYR 0.019 0.002 TYR A 463 ARG 0.006 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 169 time to evaluate : 1.594 Fit side-chains REVERT: A 118 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6845 (mmmt) REVERT: A 190 GLU cc_start: 0.6035 (mm-30) cc_final: 0.5318 (mm-30) REVERT: A 226 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6536 (mm) REVERT: A 234 GLN cc_start: 0.6557 (mm-40) cc_final: 0.5981 (mp10) REVERT: A 343 LYS cc_start: 0.6940 (mmtt) cc_final: 0.6314 (mttm) REVERT: C 11 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: D 16 GLN cc_start: 0.7289 (tt0) cc_final: 0.7005 (tp40) REVERT: D 18 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7142 (tp) REVERT: D 65 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6904 (mmp80) REVERT: D 84 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7469 (ptt-90) REVERT: B 64 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6572 (mp) REVERT: B 66 ASN cc_start: 0.6659 (OUTLIER) cc_final: 0.6454 (t0) REVERT: B 272 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6818 (mp0) outliers start: 105 outliers final: 89 residues processed: 251 average time/residue: 0.2239 time to fit residues: 83.6319 Evaluate side-chains 261 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 165 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 158 ASN A 375 HIS F 36 ASN B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12800 Z= 0.246 Angle : 0.602 9.482 17355 Z= 0.304 Chirality : 0.042 0.188 1979 Planarity : 0.004 0.041 2142 Dihedral : 7.470 86.132 1995 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.48 % Allowed : 26.15 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1558 helix: 0.62 (0.21), residues: 638 sheet: -0.55 (0.31), residues: 278 loop : -2.22 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.004 0.001 HIS A 40 PHE 0.028 0.002 PHE A 385 TYR 0.017 0.001 TYR A 463 ARG 0.005 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 169 time to evaluate : 1.430 Fit side-chains REVERT: A 118 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6850 (mmmt) REVERT: A 190 GLU cc_start: 0.5943 (mm-30) cc_final: 0.5190 (mm-30) REVERT: A 226 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6557 (mm) REVERT: A 234 GLN cc_start: 0.6524 (mm-40) cc_final: 0.5950 (mp10) REVERT: A 278 GLU cc_start: 0.4281 (OUTLIER) cc_final: 0.3949 (mt-10) REVERT: A 343 LYS cc_start: 0.6898 (mmtt) cc_final: 0.6301 (mttm) REVERT: C 11 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: D 6 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7276 (pt0) REVERT: D 16 GLN cc_start: 0.7215 (tt0) cc_final: 0.6978 (tp40) REVERT: D 18 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7168 (tp) REVERT: D 65 ARG cc_start: 0.7064 (tpm170) cc_final: 0.6839 (mmp80) REVERT: D 84 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7466 (ptt-90) REVERT: B 64 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6496 (mp) REVERT: B 66 ASN cc_start: 0.6630 (OUTLIER) cc_final: 0.6416 (t0) REVERT: B 272 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6858 (mp0) outliers start: 101 outliers final: 86 residues processed: 247 average time/residue: 0.2269 time to fit residues: 83.3159 Evaluate side-chains 260 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 165 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 651 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 158 ASN F 36 ASN B 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12800 Z= 0.177 Angle : 0.566 8.545 17355 Z= 0.286 Chirality : 0.041 0.197 1979 Planarity : 0.004 0.040 2142 Dihedral : 7.159 81.287 1995 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.30 % Allowed : 27.26 % Favored : 66.44 % 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: -0.85 (0.22), residues: 1558 helix: 0.85 (0.21), residues: 636 sheet: -0.46 (0.31), residues: 278 loop : -2.10 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 35 HIS 0.004 0.001 HIS A 40 PHE 0.016 0.001 PHE F 79 TYR 0.016 0.001 TYR A 463 ARG 0.005 0.000 ARG E 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 174 time to evaluate : 1.449 Fit side-chains REVERT: A 118 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6833 (mmmt) REVERT: A 163 ARG cc_start: 0.7465 (mtp180) cc_final: 0.7242 (mtp180) REVERT: A 190 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5224 (mm-30) REVERT: A 226 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6515 (mm) REVERT: A 234 GLN cc_start: 0.6496 (mm-40) cc_final: 0.5954 (mp10) REVERT: A 278 GLU cc_start: 0.4225 (OUTLIER) cc_final: 0.3944 (mt-10) REVERT: A 343 LYS cc_start: 0.6806 (mmtt) cc_final: 0.6286 (mttm) REVERT: C 11 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5809 (m-80) REVERT: D 6 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: D 16 GLN cc_start: 0.7194 (tt0) cc_final: 0.6971 (tp40) REVERT: D 18 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7118 (tp) REVERT: D 65 ARG cc_start: 0.7064 (tpm170) cc_final: 0.6842 (mmp80) REVERT: D 84 ARG cc_start: 0.7704 (ptp90) cc_final: 0.7464 (ptt-90) REVERT: B 64 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6451 (mp) REVERT: B 272 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6494 (mm-30) outliers start: 85 outliers final: 71 residues processed: 242 average time/residue: 0.2337 time to fit residues: 84.9087 Evaluate side-chains 252 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 173 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain C residue 11 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 15 SER Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 651 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.0040 chunk 125 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 158 ASN A 375 HIS F 36 ASN B 41 ASN B 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.138467 restraints weight = 16463.091| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.20 r_work: 0.3282 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12800 Z= 0.322 Angle : 0.646 9.859 17355 Z= 0.326 Chirality : 0.044 0.188 1979 Planarity : 0.004 0.042 2142 Dihedral : 7.457 88.037 1994 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 6.44 % Allowed : 27.48 % Favored : 66.07 % 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: -1.01 (0.21), residues: 1558 helix: 0.70 (0.21), residues: 636 sheet: -0.50 (0.31), residues: 278 loop : -2.18 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 35 HIS 0.006 0.001 HIS A 40 PHE 0.020 0.002 PHE F 99 TYR 0.024 0.002 TYR B 463 ARG 0.007 0.000 ARG E 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2823.67 seconds wall clock time: 52 minutes 23.36 seconds (3143.36 seconds total)