Starting phenix.real_space_refine on Mon Feb 19 20:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwa_35051/02_2024/8hwa_35051_updated.pdb" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 534": "OD1" <-> "OD2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "B PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 382": "OE1" <-> "OE2" Residue "D ASP 398": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D ASP 603": "OD1" <-> "OD2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D ASP 656": "OD1" <-> "OD2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E ASP 346": "OD1" <-> "OD2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "E PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 603": "OD1" <-> "OD2" Residue "E ASP 614": "OD1" <-> "OD2" Residue "E GLU 637": "OE1" <-> "OE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F ASP 58": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 245": "OD1" <-> "OD2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "F GLU 474": "OE1" <-> "OE2" Residue "F GLU 480": "OE1" <-> "OE2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ASP 74": "OD1" <-> "OD2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 104": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "K PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "E" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.49, per 1000 atoms: 0.52 Number of scatterers: 25740 At special positions: 0 Unit cell: (125.925, 128.115, 173.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS E 385 " 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 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 4.7 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 36 sheets defined 35.1% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'A' and resid 21 through 24 No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.533A pdb=" N GLU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 104 removed outlier: 3.580A pdb=" N ILE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 144 through 159 removed outlier: 4.714A pdb=" N ARG A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 364 through 374 removed outlier: 5.188A pdb=" N HIS A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.879A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 542 through 547 removed outlier: 4.843A pdb=" N MET A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 615 through 618 No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 633 through 640 removed outlier: 4.599A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 removed outlier: 4.061A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 364 through 374 removed outlier: 4.854A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.695A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 384' Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 477 through 489 removed outlier: 3.997A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 542 through 547 removed outlier: 4.543A pdb=" N MET B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.722A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 removed outlier: 3.784A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 620' Processing helix chain 'B' and resid 633 through 640 removed outlier: 3.715A pdb=" N ARG B 636 " --> pdb=" O PRO B 633 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 638 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 694 through 700 removed outlier: 3.868A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 364 through 374 removed outlier: 5.168A pdb=" N HIS C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLN C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.962A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 383' Processing helix chain 'C' and resid 386 through 398 removed outlier: 3.516A pdb=" N ASP C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.529A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 476 through 490 removed outlier: 3.899A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.817A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.840A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 694 through 698 Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 364 through 374 removed outlier: 4.899A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.941A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 383' Processing helix chain 'D' and resid 386 through 397 Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 476 through 489 removed outlier: 3.949A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.969A pdb=" N THR D 533 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 removed outlier: 3.930A pdb=" N MET D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 575 Processing helix chain 'D' and resid 615 through 618 No H-bonds generated for 'chain 'D' and resid 615 through 618' Processing helix chain 'D' and resid 633 through 640 removed outlier: 3.521A pdb=" N ARG D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 665 through 679 Processing helix chain 'D' and resid 694 through 700 removed outlier: 3.809A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 364 through 374 removed outlier: 5.133A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 4.285A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU E 383 " --> pdb=" O TYR E 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 383' Processing helix chain 'E' and resid 386 through 397 Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 468 Processing helix chain 'E' and resid 473 through 489 removed outlier: 3.984A pdb=" N LYS E 476 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS E 477 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN E 478 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 542 through 547 removed outlier: 3.933A pdb=" N MET E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 578 removed outlier: 3.706A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 641 removed outlier: 3.621A pdb=" N ARG E 636 " --> pdb=" O PRO E 633 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 660 removed outlier: 3.744A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 665 through 679 Processing helix chain 'E' and resid 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 694 through 697 No H-bonds generated for 'chain 'E' and resid 694 through 697' Processing helix chain 'F' and resid 3 through 6 No H-bonds generated for 'chain 'F' and resid 3 through 6' Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 37 through 46 Processing helix chain 'F' and resid 79 through 103 removed outlier: 3.977A pdb=" N GLN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP F 88 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 144 through 158 removed outlier: 3.503A pdb=" N LYS F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 227 through 230 No H-bonds generated for 'chain 'F' and resid 227 through 230' Processing helix chain 'F' and resid 243 through 253 removed outlier: 3.511A pdb=" N ILE F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 263 No H-bonds generated for 'chain 'F' and resid 261 through 263' Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 364 through 374 removed outlier: 5.051A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 382 removed outlier: 4.869A pdb=" N SER F 381 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 398 removed outlier: 3.520A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 434 No H-bonds generated for 'chain 'F' and resid 432 through 434' Processing helix chain 'F' and resid 456 through 468 Processing helix chain 'F' and resid 473 through 489 removed outlier: 3.660A pdb=" N LYS F 476 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS F 477 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN F 478 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 520 Processing helix chain 'F' and resid 529 through 531 No H-bonds generated for 'chain 'F' and resid 529 through 531' Processing helix chain 'F' and resid 542 through 545 No H-bonds generated for 'chain 'F' and resid 542 through 545' Processing helix chain 'F' and resid 571 through 576 Processing helix chain 'F' and resid 615 through 618 No H-bonds generated for 'chain 'F' and resid 615 through 618' Processing helix chain 'F' and resid 633 through 641 removed outlier: 4.934A pdb=" N GLU F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 658 No H-bonds generated for 'chain 'F' and resid 655 through 658' Processing helix chain 'F' and resid 665 through 679 Processing helix chain 'F' and resid 690 through 692 No H-bonds generated for 'chain 'F' and resid 690 through 692' Processing helix chain 'F' and resid 694 through 698 Processing helix chain 'K' and resid 4 through 6 No H-bonds generated for 'chain 'K' and resid 4 through 6' Processing helix chain 'K' and resid 21 through 26 Processing helix chain 'K' and resid 37 through 46 removed outlier: 3.550A pdb=" N GLU K 41 " --> pdb=" O CYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 103 Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 144 through 158 removed outlier: 4.710A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 167 No H-bonds generated for 'chain 'K' and resid 164 through 167' Processing helix chain 'K' and resid 204 through 206 No H-bonds generated for 'chain 'K' and resid 204 through 206' Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 removed outlier: 3.774A pdb=" N PHE A 12 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.647A pdb=" N TYR A 219 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N THR A 143 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N PHE A 221 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 68 through 71 Processing sheet with id= D, first strand: chain 'A' and resid 123 through 125 Processing sheet with id= E, first strand: chain 'A' and resid 302 through 305 Processing sheet with id= F, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= G, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.592A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 621 through 626 removed outlier: 5.941A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY A 503 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 553 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 629 through 631 Processing sheet with id= J, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.577A pdb=" N LEU B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.673A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 621 through 626 removed outlier: 6.042A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 503 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= N, first strand: chain 'B' and resid 629 through 631 Processing sheet with id= O, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.910A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 621 through 626 removed outlier: 6.014A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 553 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR C 527 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= R, first strand: chain 'C' and resid 629 through 631 Processing sheet with id= S, first strand: chain 'D' and resid 349 through 351 removed outlier: 3.518A pdb=" N ILE D 351 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.920A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 621 through 626 removed outlier: 5.746A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER D 556 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR D 527 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= W, first strand: chain 'D' and resid 629 through 631 Processing sheet with id= X, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.776A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 621 through 625 removed outlier: 6.110A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 600 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE E 501 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE E 602 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 629 through 631 Processing sheet with id= AA, first strand: chain 'F' and resid 11 through 14 removed outlier: 3.625A pdb=" N GLU F 33 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 123 through 125 Processing sheet with id= AC, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.704A pdb=" N LYS F 317 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.678A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 621 through 626 removed outlier: 6.058A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 600 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N PHE F 501 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 602 " --> pdb=" O PHE F 501 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY F 503 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 628 through 631 removed outlier: 7.423A pdb=" N LYS F 647 " --> pdb=" O HIS F 629 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N SER F 631 " --> pdb=" O LYS F 647 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS F 649 " --> pdb=" O SER F 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 64 through 73 removed outlier: 7.106A pdb=" N THR F 140 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N MET F 69 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N LEU F 138 " --> pdb=" O MET F 69 " (cutoff:3.500A) removed outlier: 11.973A pdb=" N VAL F 71 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 11.109A pdb=" N ILE F 136 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 12.330A pdb=" N LEU F 73 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 11.502A pdb=" N HIS F 134 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 11 through 13 removed outlier: 3.520A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AJ, first strand: chain 'K' and resid 64 through 73 removed outlier: 6.911A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 12.129A pdb=" N MET K 69 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N LEU K 138 " --> pdb=" O MET K 69 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N VAL K 71 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ILE K 136 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 12.810A pdb=" N LEU K 73 " --> pdb=" O HIS K 134 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N HIS K 134 " --> pdb=" O LEU K 73 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1779 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: 8.79 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6095 1.33 - 1.45: 5196 1.45 - 1.57: 14744 1.57 - 1.70: 39 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" N ASP F 431 " pdb=" CA ASP F 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N LEU B 700 " pdb=" CA LEU B 700 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.32e-02 5.74e+03 4.89e+00 bond pdb=" N ASP D 656 " pdb=" CA ASP D 656 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.33e-02 5.65e+03 4.83e+00 bond pdb=" N LEU C 700 " pdb=" CA LEU C 700 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.50e-02 4.44e+03 4.60e+00 bond pdb=" N ASP A 277 " pdb=" CA ASP A 277 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.52e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 99.56 - 107.62: 968 107.62 - 115.67: 16205 115.67 - 123.72: 17830 123.72 - 131.77: 552 131.77 - 139.82: 38 Bond angle restraints: 35593 Sorted by residual: angle pdb=" N LEU B 700 " pdb=" CA LEU B 700 " pdb=" C LEU B 700 " ideal model delta sigma weight residual 113.50 107.98 5.52 1.23e+00 6.61e-01 2.01e+01 angle pdb=" N LEU C 700 " pdb=" CA LEU C 700 " pdb=" C LEU C 700 " ideal model delta sigma weight residual 114.39 108.05 6.34 1.45e+00 4.76e-01 1.91e+01 angle pdb=" CB MET F 116 " pdb=" CG MET F 116 " pdb=" SD MET F 116 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N LEU E 700 " pdb=" CA LEU E 700 " pdb=" C LEU E 700 " ideal model delta sigma weight residual 113.37 107.87 5.50 1.38e+00 5.25e-01 1.59e+01 angle pdb=" CA GLU E 557 " pdb=" CB GLU E 557 " pdb=" CG GLU E 557 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 15428 31.32 - 62.64: 656 62.64 - 93.95: 46 93.95 - 125.27: 0 125.27 - 156.59: 2 Dihedral angle restraints: 16132 sinusoidal: 6841 harmonic: 9291 Sorted by residual: dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS E 385 " pdb=" CB CYS E 385 " ideal model delta sinusoidal sigma weight residual -86.00 -23.24 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.41 156.59 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.24 152.76 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2714 0.036 - 0.073: 908 0.073 - 0.109: 308 0.109 - 0.145: 50 0.145 - 0.182: 4 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU B 700 " pdb=" N LEU B 700 " pdb=" C LEU B 700 " pdb=" CB LEU B 700 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB ILE F 681 " pdb=" CA ILE F 681 " pdb=" CG1 ILE F 681 " pdb=" CG2 ILE F 681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA LEU E 700 " pdb=" N LEU E 700 " pdb=" C LEU E 700 " pdb=" CB LEU E 700 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 236 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.46e+01 pdb=" C TRP A 236 " -0.066 2.00e-02 2.50e+03 pdb=" O TRP A 236 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 237 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 361 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 362 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 375 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO F 376 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 376 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 376 " 0.030 5.00e-02 4.00e+02 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 182 2.55 - 3.13: 19583 3.13 - 3.72: 38532 3.72 - 4.31: 52287 4.31 - 4.90: 87370 Nonbonded interactions: 197954 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.956 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 2.005 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.023 2.170 nonbonded pdb=" O1A ATP D1001 " pdb="MG MG D1002 " model vdw 2.031 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.044 2.170 ... (remaining 197949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 700) selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = (chain 'D' and resid 323 through 701) selection = (chain 'E' and resid 323 through 701) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.410 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 66.770 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26281 Z= 0.169 Angle : 0.583 12.570 35593 Z= 0.328 Chirality : 0.041 0.182 3984 Planarity : 0.004 0.058 4537 Dihedral : 16.332 156.590 10087 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 0.35 % Allowed : 15.50 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.15 (0.15), residues: 3133 helix: 0.54 (0.16), residues: 1073 sheet: -1.39 (0.25), residues: 454 loop : -1.48 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.003 0.000 HIS B 629 PHE 0.018 0.001 PHE D 698 TYR 0.020 0.001 TYR D 664 ARG 0.006 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 684 MET cc_start: 0.8370 (tmm) cc_final: 0.7876 (tmm) REVERT: F 138 LEU cc_start: 0.7020 (mp) cc_final: 0.6584 (pt) REVERT: F 322 ASP cc_start: 0.7504 (t70) cc_final: 0.7051 (t70) REVERT: F 684 MET cc_start: 0.7655 (tpp) cc_final: 0.6494 (tpp) outliers start: 10 outliers final: 1 residues processed: 231 average time/residue: 0.4003 time to fit residues: 144.5511 Evaluate side-chains 203 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 181 optimal weight: 0.0470 chunk 282 optimal weight: 10.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN B 466 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN E 529 GLN F 95 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 26281 Z= 0.430 Angle : 0.637 8.021 35593 Z= 0.331 Chirality : 0.045 0.174 3984 Planarity : 0.005 0.058 4537 Dihedral : 10.122 158.631 3668 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 3.43 % Allowed : 15.16 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.57 (0.15), residues: 3133 helix: 0.06 (0.16), residues: 1075 sheet: -1.70 (0.24), residues: 462 loop : -1.59 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 350 HIS 0.008 0.001 HIS F 680 PHE 0.022 0.002 PHE F 630 TYR 0.030 0.002 TYR C 482 ARG 0.009 0.001 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 212 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (m-30) REVERT: C 325 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8399 (ttmt) REVERT: C 471 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9333 (pp) REVERT: E 382 GLU cc_start: 0.7618 (mp0) cc_final: 0.7256 (mp0) REVERT: F 109 HIS cc_start: 0.7262 (t-90) cc_final: 0.7015 (t-90) REVERT: F 194 ILE cc_start: 0.8996 (pt) cc_final: 0.8675 (mm) REVERT: F 321 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8810 (pp) REVERT: F 322 ASP cc_start: 0.8014 (t70) cc_final: 0.7754 (t70) REVERT: F 332 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8121 (ttm-80) REVERT: F 363 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9064 (mp) REVERT: K 40 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8460 (tt) outliers start: 99 outliers final: 65 residues processed: 292 average time/residue: 0.3637 time to fit residues: 168.5443 Evaluate side-chains 260 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 189 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 701 LYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 215 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 305 optimal weight: 0.0970 chunk 251 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN B 466 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN F 95 ASN F 198 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS F 632 GLN F 641 ASN ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26281 Z= 0.156 Angle : 0.496 9.816 35593 Z= 0.256 Chirality : 0.041 0.159 3984 Planarity : 0.004 0.054 4537 Dihedral : 9.638 156.887 3667 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 2.71 % Allowed : 16.51 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.17 (0.15), residues: 3133 helix: 0.44 (0.16), residues: 1070 sheet: -1.45 (0.24), residues: 470 loop : -1.40 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.014 0.001 HIS A 195 PHE 0.012 0.001 PHE A 243 TYR 0.017 0.001 TYR B 482 ARG 0.003 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 214 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7756 (ttp80) cc_final: 0.7095 (ttp80) REVERT: B 572 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: C 325 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8224 (ttpt) REVERT: C 471 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9287 (pp) REVERT: D 660 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: E 529 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: E 660 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: F 109 HIS cc_start: 0.7214 (t-90) cc_final: 0.7001 (t-90) REVERT: F 194 ILE cc_start: 0.9006 (pt) cc_final: 0.8709 (mm) REVERT: F 322 ASP cc_start: 0.7754 (t70) cc_final: 0.7332 (t70) REVERT: F 332 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8263 (ttm-80) outliers start: 78 outliers final: 40 residues processed: 277 average time/residue: 0.3689 time to fit residues: 162.9247 Evaluate side-chains 241 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 283 optimal weight: 0.1980 chunk 300 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 269 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 195 HIS A 478 ASN B 466 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN F 95 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS F 629 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26281 Z= 0.269 Angle : 0.538 8.982 35593 Z= 0.277 Chirality : 0.042 0.205 3984 Planarity : 0.004 0.055 4537 Dihedral : 9.581 157.925 3667 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 3.85 % Allowed : 17.03 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.24 (0.15), residues: 3133 helix: 0.43 (0.16), residues: 1070 sheet: -1.55 (0.24), residues: 464 loop : -1.46 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.003 0.001 HIS F 347 PHE 0.015 0.001 PHE D 698 TYR 0.022 0.001 TYR A 482 ARG 0.014 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 212 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2731 (ttt) cc_final: 0.2484 (ttm) REVERT: B 572 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: C 325 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8332 (ttmt) REVERT: C 471 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9291 (pp) REVERT: D 660 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: E 382 GLU cc_start: 0.7629 (mp0) cc_final: 0.7161 (mp0) REVERT: E 529 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: E 660 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8479 (mp10) REVERT: F 109 HIS cc_start: 0.7261 (t-90) cc_final: 0.6954 (t70) REVERT: F 194 ILE cc_start: 0.9023 (pt) cc_final: 0.8739 (mm) REVERT: F 288 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (tpt90) REVERT: F 322 ASP cc_start: 0.7838 (t70) cc_final: 0.7433 (t70) REVERT: F 332 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8303 (ttm-80) REVERT: F 363 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9041 (mp) REVERT: F 684 MET cc_start: 0.8071 (tpp) cc_final: 0.7467 (tpp) REVERT: K 40 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8428 (tt) outliers start: 111 outliers final: 74 residues processed: 305 average time/residue: 0.3713 time to fit residues: 181.5713 Evaluate side-chains 276 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 193 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 153 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 195 HIS A 478 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26281 Z= 0.349 Angle : 0.578 10.684 35593 Z= 0.297 Chirality : 0.043 0.178 3984 Planarity : 0.004 0.056 4537 Dihedral : 9.613 157.946 3667 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 4.58 % Allowed : 17.38 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.35 (0.15), residues: 3133 helix: 0.30 (0.16), residues: 1065 sheet: -1.56 (0.24), residues: 464 loop : -1.50 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.009 0.001 HIS A 195 PHE 0.015 0.001 PHE D 626 TYR 0.028 0.001 TYR A 482 ARG 0.007 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 198 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5264 (OUTLIER) cc_final: 0.4901 (p0) REVERT: A 99 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7042 (ttp80) REVERT: C 471 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9304 (pp) REVERT: C 579 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7688 (mt-10) REVERT: D 660 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: E 382 GLU cc_start: 0.7664 (mp0) cc_final: 0.7159 (mp0) REVERT: E 529 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: E 660 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: F 69 MET cc_start: 0.7851 (mmm) cc_final: 0.7564 (mmm) REVERT: F 109 HIS cc_start: 0.7277 (t-90) cc_final: 0.7064 (t-90) REVERT: F 288 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8665 (tpt90) REVERT: F 321 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8769 (pp) REVERT: F 332 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8166 (ttm-80) REVERT: F 363 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9065 (mp) REVERT: F 383 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9314 (mp) REVERT: F 474 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.5119 (pt0) REVERT: K 40 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 132 outliers final: 90 residues processed: 309 average time/residue: 0.3625 time to fit residues: 178.1552 Evaluate side-chains 295 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 193 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 383 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 662 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.0670 chunk 270 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 74 optimal weight: 0.0470 chunk 300 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN F 95 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26281 Z= 0.147 Angle : 0.497 11.299 35593 Z= 0.255 Chirality : 0.041 0.180 3984 Planarity : 0.004 0.053 4537 Dihedral : 9.300 157.463 3667 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 2.98 % Allowed : 19.22 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.02 (0.15), residues: 3133 helix: 0.55 (0.16), residues: 1065 sheet: -1.34 (0.24), residues: 481 loop : -1.30 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.024 0.001 HIS A 109 PHE 0.011 0.001 PHE D 698 TYR 0.019 0.001 TYR A 482 ARG 0.005 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 218 time to evaluate : 3.395 Fit side-chains revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4861 (p0) REVERT: A 99 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7029 (ttp80) REVERT: B 557 GLU cc_start: 0.7148 (mp0) cc_final: 0.6923 (mp0) REVERT: C 471 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9290 (pp) REVERT: C 660 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: D 660 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: E 382 GLU cc_start: 0.7503 (mp0) cc_final: 0.7071 (mp0) REVERT: E 529 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7451 (pp30) REVERT: E 660 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8453 (mp10) REVERT: F 1 MET cc_start: 0.2364 (ttt) cc_final: 0.2131 (ttt) REVERT: F 69 MET cc_start: 0.7853 (mmm) cc_final: 0.7542 (mmm) REVERT: F 109 HIS cc_start: 0.7227 (t-90) cc_final: 0.7020 (t-90) REVERT: F 288 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8635 (tpt90) REVERT: F 474 GLU cc_start: 0.5037 (OUTLIER) cc_final: 0.4781 (pt0) REVERT: K 40 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8381 (tt) outliers start: 86 outliers final: 56 residues processed: 285 average time/residue: 0.3961 time to fit residues: 178.7336 Evaluate side-chains 264 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 199 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 529 GLN Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 253 optimal weight: 0.0980 chunk 168 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A 529 GLN B 548 HIS ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26281 Z= 0.138 Angle : 0.494 11.084 35593 Z= 0.252 Chirality : 0.040 0.224 3984 Planarity : 0.003 0.054 4537 Dihedral : 9.156 157.630 3667 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.81 % Allowed : 19.39 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.91 (0.15), residues: 3133 helix: 0.59 (0.16), residues: 1084 sheet: -1.16 (0.25), residues: 466 loop : -1.25 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP A 350 HIS 0.011 0.001 HIS A 109 PHE 0.011 0.001 PHE E 561 TYR 0.017 0.001 TYR B 482 ARG 0.005 0.000 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 221 time to evaluate : 3.368 Fit side-chains revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5479 (OUTLIER) cc_final: 0.4976 (p0) REVERT: C 471 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9250 (pp) REVERT: C 656 ASP cc_start: 0.8332 (p0) cc_final: 0.8065 (p0) REVERT: C 660 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: D 660 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: D 684 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7066 (tmm) REVERT: E 382 GLU cc_start: 0.7561 (mp0) cc_final: 0.7095 (mp0) REVERT: E 426 MET cc_start: 0.7344 (mmm) cc_final: 0.7006 (mmm) REVERT: E 618 MET cc_start: 0.8048 (mmp) cc_final: 0.7564 (mmp) REVERT: E 660 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: F 69 MET cc_start: 0.7856 (mmm) cc_final: 0.7549 (mmm) REVERT: F 194 ILE cc_start: 0.8982 (pt) cc_final: 0.8735 (mm) REVERT: F 288 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8613 (tpt90) REVERT: F 321 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8581 (pp) REVERT: F 332 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8266 (ttm-80) REVERT: F 474 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4915 (pt0) REVERT: K 40 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 81 outliers final: 54 residues processed: 285 average time/residue: 0.3744 time to fit residues: 170.8925 Evaluate side-chains 269 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 204 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 179 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 235 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26281 Z= 0.133 Angle : 0.492 11.721 35593 Z= 0.249 Chirality : 0.040 0.218 3984 Planarity : 0.003 0.053 4537 Dihedral : 9.036 157.648 3667 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 19.53 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.79 (0.15), residues: 3133 helix: 0.67 (0.16), residues: 1083 sheet: -1.07 (0.25), residues: 466 loop : -1.18 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.012 0.001 HIS A 109 PHE 0.012 0.001 PHE A 243 TYR 0.017 0.001 TYR B 482 ARG 0.008 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 217 time to evaluate : 2.829 Fit side-chains REVERT: A 8 ASN cc_start: 0.5618 (OUTLIER) cc_final: 0.5113 (p0) REVERT: A 99 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7123 (ttp80) REVERT: A 651 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8734 (tp) REVERT: C 471 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9240 (pp) REVERT: C 656 ASP cc_start: 0.8440 (p0) cc_final: 0.8199 (p0) REVERT: C 660 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: D 660 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: D 684 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.6980 (tmm) REVERT: E 382 GLU cc_start: 0.7557 (mp0) cc_final: 0.7094 (mp0) REVERT: E 618 MET cc_start: 0.8081 (mmp) cc_final: 0.7665 (mmp) REVERT: E 660 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: E 684 MET cc_start: 0.8271 (tmm) cc_final: 0.7783 (tmm) REVERT: F 69 MET cc_start: 0.7791 (mmm) cc_final: 0.7480 (mmm) REVERT: F 194 ILE cc_start: 0.8969 (pt) cc_final: 0.8716 (mm) REVERT: F 252 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8474 (ttmm) REVERT: F 288 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8578 (tpt90) REVERT: F 321 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8523 (pp) REVERT: F 332 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8329 (ttm-80) REVERT: F 474 GLU cc_start: 0.5201 (OUTLIER) cc_final: 0.5000 (pt0) REVERT: K 40 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8384 (tt) outliers start: 83 outliers final: 61 residues processed: 283 average time/residue: 0.3961 time to fit residues: 179.4446 Evaluate side-chains 280 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 206 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 474 GLU Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 4.9990 chunk 262 optimal weight: 0.6980 chunk 279 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 573 ASN E 529 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26281 Z= 0.143 Angle : 0.500 12.093 35593 Z= 0.251 Chirality : 0.041 0.216 3984 Planarity : 0.004 0.053 4537 Dihedral : 8.949 157.751 3667 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.74 % Allowed : 19.84 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 3133 helix: 0.69 (0.16), residues: 1084 sheet: -0.98 (0.25), residues: 467 loop : -1.13 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.008 0.001 HIS A 109 PHE 0.016 0.001 PHE A 100 TYR 0.017 0.001 TYR B 482 ARG 0.011 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 217 time to evaluate : 3.048 Fit side-chains REVERT: A 8 ASN cc_start: 0.5626 (OUTLIER) cc_final: 0.5129 (p0) REVERT: A 99 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7123 (ttp80) REVERT: A 651 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (tp) REVERT: C 471 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9236 (pp) REVERT: C 656 ASP cc_start: 0.8448 (p0) cc_final: 0.8210 (p0) REVERT: C 660 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: D 660 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: D 684 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.6973 (tmm) REVERT: E 382 GLU cc_start: 0.7591 (mp0) cc_final: 0.7108 (mp0) REVERT: E 529 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7377 (pp30) REVERT: E 618 MET cc_start: 0.8090 (mmp) cc_final: 0.7683 (mmp) REVERT: E 660 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: F 194 ILE cc_start: 0.8983 (pt) cc_final: 0.8743 (mm) REVERT: F 252 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (ttmm) REVERT: F 288 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8569 (mmm160) REVERT: F 321 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8595 (pp) REVERT: F 332 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8267 (ttm-80) REVERT: K 1 MET cc_start: 0.1607 (tpt) cc_final: 0.1033 (tpt) REVERT: K 40 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8397 (tt) outliers start: 79 outliers final: 60 residues processed: 279 average time/residue: 0.3708 time to fit residues: 165.1029 Evaluate side-chains 279 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 206 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 252 LYS Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 190 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 478 ASN D 529 GLN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26281 Z= 0.181 Angle : 0.522 11.910 35593 Z= 0.261 Chirality : 0.041 0.333 3984 Planarity : 0.004 0.053 4537 Dihedral : 8.880 157.890 3667 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 2.67 % Allowed : 20.01 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.72 (0.15), residues: 3133 helix: 0.67 (0.16), residues: 1085 sheet: -0.95 (0.25), residues: 462 loop : -1.13 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.004 0.001 HIS A 109 PHE 0.015 0.001 PHE A 100 TYR 0.018 0.001 TYR B 482 ARG 0.008 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 213 time to evaluate : 3.090 Fit side-chains revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5611 (OUTLIER) cc_final: 0.5112 (p0) REVERT: A 99 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7078 (ttp80) REVERT: C 471 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9243 (pp) REVERT: C 660 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: D 660 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: D 684 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7017 (tmm) REVERT: E 382 GLU cc_start: 0.7560 (mp0) cc_final: 0.7087 (mp0) REVERT: E 426 MET cc_start: 0.7360 (mmm) cc_final: 0.7044 (mmm) REVERT: E 529 GLN cc_start: 0.8029 (pp30) cc_final: 0.7407 (pp30) REVERT: E 595 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8213 (mtt180) REVERT: E 618 MET cc_start: 0.8116 (mmp) cc_final: 0.7688 (mmp) REVERT: E 660 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: F 194 ILE cc_start: 0.8984 (pt) cc_final: 0.8757 (mm) REVERT: F 288 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8566 (mmm160) REVERT: F 321 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8619 (pp) REVERT: F 332 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8283 (ttm-80) REVERT: K 1 MET cc_start: 0.1829 (tpt) cc_final: 0.1264 (tpt) outliers start: 77 outliers final: 59 residues processed: 273 average time/residue: 0.3896 time to fit residues: 169.2985 Evaluate side-chains 274 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 205 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 402 ASP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 402 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 595 ARG Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 247 ILE Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 216 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 478 ASN D 546 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083320 restraints weight = 56283.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086866 restraints weight = 30349.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087347 restraints weight = 17822.182| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26281 Z= 0.152 Angle : 0.519 11.800 35593 Z= 0.258 Chirality : 0.041 0.278 3984 Planarity : 0.004 0.052 4537 Dihedral : 8.664 157.788 3667 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 2.64 % Allowed : 19.94 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.69 (0.15), residues: 3133 helix: 0.66 (0.16), residues: 1090 sheet: -0.85 (0.25), residues: 462 loop : -1.11 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.006 0.001 HIS A 109 PHE 0.014 0.001 PHE A 100 TYR 0.017 0.001 TYR B 482 ARG 0.011 0.000 ARG B 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.54 seconds wall clock time: 86 minutes 58.10 seconds (5218.10 seconds total)