Starting phenix.real_space_refine on Fri Feb 23 11:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vh6_31988/02_2024/7vh6_31988_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 57 5.49 5 S 162 5.16 5 Be 6 3.05 5 C 25206 2.51 5 N 5859 2.21 5 O 6894 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 140": "OD1" <-> "OD2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ARG 215": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 659": "NH1" <-> "NH2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 811": "NH1" <-> "NH2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 511": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 659": "NH1" <-> "NH2" Residue "C TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 811": "NH1" <-> "NH2" Residue "D ASP 140": "OD1" <-> "OD2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "D ARG 215": "NH1" <-> "NH2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 511": "NH1" <-> "NH2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 659": "NH1" <-> "NH2" Residue "D TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D ARG 754": "NH1" <-> "NH2" Residue "D PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 811": "NH1" <-> "NH2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ASP 213": "OD1" <-> "OD2" Residue "E ARG 215": "NH1" <-> "NH2" Residue "E ASP 226": "OD1" <-> "OD2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 315": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E ARG 414": "NH1" <-> "NH2" Residue "E TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 469": "NH1" <-> "NH2" Residue "E ARG 511": "NH1" <-> "NH2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E ARG 617": "NH1" <-> "NH2" Residue "E ARG 659": "NH1" <-> "NH2" Residue "E TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 695": "NH1" <-> "NH2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 811": "NH1" <-> "NH2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F ASP 226": "OD1" <-> "OD2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "F GLU 397": "OE1" <-> "OE2" Residue "F ARG 414": "NH1" <-> "NH2" Residue "F TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 469": "NH1" <-> "NH2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ARG 553": "NH1" <-> "NH2" Residue "F ARG 617": "NH1" <-> "NH2" Residue "F ARG 659": "NH1" <-> "NH2" Residue "F TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 695": "NH1" <-> "NH2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 811": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38202 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "B" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "C" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "D" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "E" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "F" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "A" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 576 Unusual residues: {'BEF': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 524 Unusual residues: {'BEF': 1, 'POV': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 18.67, per 1000 atoms: 0.49 Number of scatterers: 38202 At special positions: 0 Unit cell: (139.36, 189.28, 193.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 57 15.00 F 18 9.00 O 6894 8.00 N 5859 7.00 C 25206 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.45 Conformation dependent library (CDL) restraints added in 6.1 seconds 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 42 sheets defined 53.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.58 Creating SS restraints... Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.666A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 172 removed outlier: 3.788A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.636A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.782A pdb=" N ILE A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.611A pdb=" N THR A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.714A pdb=" N GLU A 367 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 410 removed outlier: 4.305A pdb=" N MET A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 removed outlier: 4.001A pdb=" N ALA A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 435 through 440' Processing helix chain 'A' and resid 477 through 481 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 538 through 549 removed outlier: 4.141A pdb=" N GLN A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 595 through 603 Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.541A pdb=" N LEU A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 672 through 713 removed outlier: 3.541A pdb=" N LEU A 678 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 679 " --> pdb=" O ASP A 676 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 680 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 689 " --> pdb=" O HIS A 686 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 690 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 692 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 695 " --> pdb=" O VAL A 692 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 696 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 703 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 706 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 708 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 710 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A 712 " --> pdb=" O TRP A 709 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 713 " --> pdb=" O ILE A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 736 removed outlier: 3.552A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 776 Processing helix chain 'A' and resid 791 through 810 removed outlier: 3.579A pdb=" N MET A 795 " --> pdb=" O MET A 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE A 808 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.732A pdb=" N THR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 877 Processing helix chain 'A' and resid 880 through 887 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.666A pdb=" N VAL B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 172 removed outlier: 3.788A pdb=" N ILE B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.636A pdb=" N LEU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.781A pdb=" N ILE B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.610A pdb=" N THR B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.714A pdb=" N GLU B 367 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 410 removed outlier: 4.289A pdb=" N MET B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 removed outlier: 4.020A pdb=" N ALA B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 435 through 440' Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 538 through 549 removed outlier: 4.140A pdb=" N GLN B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.541A pdb=" N LEU B 622 " --> pdb=" O VAL B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 644 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 672 through 713 removed outlier: 3.542A pdb=" N LEU B 678 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 679 " --> pdb=" O ASP B 676 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 680 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 689 " --> pdb=" O HIS B 686 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 690 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 692 " --> pdb=" O TYR B 689 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 695 " --> pdb=" O VAL B 692 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 696 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 703 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 705 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 706 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 708 " --> pdb=" O PHE B 705 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 712 " --> pdb=" O TRP B 709 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU B 713 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 736 removed outlier: 3.553A pdb=" N VAL B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 776 Processing helix chain 'B' and resid 791 through 810 removed outlier: 3.580A pdb=" N MET B 795 " --> pdb=" O MET B 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE B 808 " --> pdb=" O ASN B 804 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 842 removed outlier: 3.732A pdb=" N THR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 877 Processing helix chain 'B' and resid 880 through 887 Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.666A pdb=" N VAL C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 172 removed outlier: 3.789A pdb=" N ILE C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 278 Processing helix chain 'C' and resid 285 through 314 removed outlier: 3.637A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.781A pdb=" N ILE C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.610A pdb=" N THR C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.714A pdb=" N GLU C 367 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 410 removed outlier: 4.303A pdb=" N MET C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.024A pdb=" N ALA C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing helix chain 'C' and resid 477 through 481 Processing helix chain 'C' and resid 491 through 508 Processing helix chain 'C' and resid 538 through 549 removed outlier: 4.141A pdb=" N GLN C 542 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 584 No H-bonds generated for 'chain 'C' and resid 581 through 584' Processing helix chain 'C' and resid 595 through 603 Processing helix chain 'C' and resid 612 through 625 removed outlier: 3.542A pdb=" N LEU C 622 " --> pdb=" O VAL C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 644 Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 672 through 713 removed outlier: 3.541A pdb=" N LEU C 678 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS C 679 " --> pdb=" O ASP C 676 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR C 680 " --> pdb=" O ALA C 677 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 689 " --> pdb=" O HIS C 686 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 690 " --> pdb=" O ARG C 687 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 692 " --> pdb=" O TYR C 689 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 695 " --> pdb=" O VAL C 692 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE C 696 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 703 " --> pdb=" O LEU C 700 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 705 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU C 706 " --> pdb=" O GLU C 703 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 708 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 710 " --> pdb=" O GLY C 707 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE C 712 " --> pdb=" O TRP C 709 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 736 removed outlier: 3.553A pdb=" N VAL C 723 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA C 735 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 776 Processing helix chain 'C' and resid 791 through 810 removed outlier: 3.579A pdb=" N MET C 795 " --> pdb=" O MET C 791 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 806 " --> pdb=" O THR C 802 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE C 807 " --> pdb=" O GLU C 803 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE C 808 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 809 " --> pdb=" O TRP C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 842 removed outlier: 3.732A pdb=" N THR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 877 Processing helix chain 'C' and resid 880 through 887 Processing helix chain 'D' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.665A pdb=" N VAL D 127 " --> pdb=" O PRO D 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 172 removed outlier: 3.788A pdb=" N ILE D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 278 Processing helix chain 'D' and resid 285 through 314 removed outlier: 3.636A pdb=" N LEU D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.781A pdb=" N ILE D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.611A pdb=" N THR D 343 " --> pdb=" O PRO D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.715A pdb=" N GLU D 367 " --> pdb=" O SER D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 410 removed outlier: 4.306A pdb=" N MET D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 removed outlier: 4.011A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 435 through 440' Processing helix chain 'D' and resid 477 through 481 Processing helix chain 'D' and resid 491 through 508 Processing helix chain 'D' and resid 538 through 549 removed outlier: 4.141A pdb=" N GLN D 542 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 584 No H-bonds generated for 'chain 'D' and resid 581 through 584' Processing helix chain 'D' and resid 595 through 603 Processing helix chain 'D' and resid 612 through 625 removed outlier: 3.541A pdb=" N LEU D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 644 Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 672 through 713 removed outlier: 3.542A pdb=" N LEU D 678 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS D 679 " --> pdb=" O ASP D 676 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 680 " --> pdb=" O ALA D 677 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 689 " --> pdb=" O HIS D 686 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER D 690 " --> pdb=" O ARG D 687 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 692 " --> pdb=" O TYR D 689 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 693 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 695 " --> pdb=" O VAL D 692 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 696 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 703 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE D 705 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 706 " --> pdb=" O GLU D 703 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 708 " --> pdb=" O PHE D 705 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 712 " --> pdb=" O TRP D 709 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU D 713 " --> pdb=" O ILE D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 736 removed outlier: 3.552A pdb=" N VAL D 723 " --> pdb=" O ILE D 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D 724 " --> pdb=" O ASP D 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D 735 " --> pdb=" O VAL D 731 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 776 Processing helix chain 'D' and resid 791 through 810 removed outlier: 3.579A pdb=" N MET D 795 " --> pdb=" O MET D 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU D 806 " --> pdb=" O THR D 802 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE D 807 " --> pdb=" O GLU D 803 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE D 808 " --> pdb=" O ASN D 804 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 809 " --> pdb=" O TRP D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 842 removed outlier: 3.731A pdb=" N THR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 877 Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 removed outlier: 3.667A pdb=" N VAL E 127 " --> pdb=" O PRO E 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 172 removed outlier: 3.788A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 278 Processing helix chain 'E' and resid 285 through 314 removed outlier: 3.636A pdb=" N LEU E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.782A pdb=" N ILE E 332 " --> pdb=" O GLY E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 356 removed outlier: 3.610A pdb=" N THR E 343 " --> pdb=" O PRO E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.714A pdb=" N GLU E 367 " --> pdb=" O SER E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 410 removed outlier: 4.311A pdb=" N MET E 405 " --> pdb=" O PRO E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 440 removed outlier: 4.021A pdb=" N ALA E 439 " --> pdb=" O LYS E 435 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 435 through 440' Processing helix chain 'E' and resid 477 through 481 Processing helix chain 'E' and resid 491 through 508 Processing helix chain 'E' and resid 538 through 549 removed outlier: 4.141A pdb=" N GLN E 542 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing helix chain 'E' and resid 595 through 603 Processing helix chain 'E' and resid 612 through 625 removed outlier: 3.542A pdb=" N LEU E 622 " --> pdb=" O VAL E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 644 Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'E' and resid 672 through 713 removed outlier: 3.542A pdb=" N LEU E 678 " --> pdb=" O ILE E 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 679 " --> pdb=" O ASP E 676 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 680 " --> pdb=" O ALA E 677 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR E 689 " --> pdb=" O HIS E 686 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 690 " --> pdb=" O ARG E 687 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 692 " --> pdb=" O TYR E 689 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 693 " --> pdb=" O SER E 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 695 " --> pdb=" O VAL E 692 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 696 " --> pdb=" O VAL E 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU E 703 " --> pdb=" O LEU E 700 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE E 705 " --> pdb=" O LEU E 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU E 706 " --> pdb=" O GLU E 703 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 708 " --> pdb=" O PHE E 705 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 710 " --> pdb=" O GLY E 707 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE E 712 " --> pdb=" O TRP E 709 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU E 713 " --> pdb=" O ILE E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 736 removed outlier: 3.553A pdb=" N VAL E 723 " --> pdb=" O ILE E 719 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 724 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 733 " --> pdb=" O ALA E 729 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA E 735 " --> pdb=" O VAL E 731 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE E 736 " --> pdb=" O ALA E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 776 Processing helix chain 'E' and resid 791 through 810 removed outlier: 3.580A pdb=" N MET E 795 " --> pdb=" O MET E 791 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 806 " --> pdb=" O THR E 802 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE E 807 " --> pdb=" O GLU E 803 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE E 808 " --> pdb=" O ASN E 804 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE E 809 " --> pdb=" O TRP E 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 842 removed outlier: 3.732A pdb=" N THR E 840 " --> pdb=" O ALA E 836 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 877 Processing helix chain 'E' and resid 880 through 887 Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.541A pdb=" N MET F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 137 removed outlier: 3.666A pdb=" N VAL F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 172 removed outlier: 3.788A pdb=" N ILE F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN F 161 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 278 Processing helix chain 'F' and resid 285 through 314 removed outlier: 3.636A pdb=" N LEU F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 removed outlier: 3.782A pdb=" N ILE F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 356 removed outlier: 3.610A pdb=" N THR F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.715A pdb=" N GLU F 367 " --> pdb=" O SER F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 410 removed outlier: 4.333A pdb=" N MET F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.517A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 440 removed outlier: 4.019A pdb=" N ALA F 439 " --> pdb=" O LYS F 435 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 435 through 440' Processing helix chain 'F' and resid 477 through 481 Processing helix chain 'F' and resid 491 through 508 Processing helix chain 'F' and resid 538 through 549 removed outlier: 4.142A pdb=" N GLN F 542 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 572 removed outlier: 3.566A pdb=" N THR F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 584 No H-bonds generated for 'chain 'F' and resid 581 through 584' Processing helix chain 'F' and resid 595 through 603 Processing helix chain 'F' and resid 612 through 625 removed outlier: 3.541A pdb=" N LEU F 622 " --> pdb=" O VAL F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 644 Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'F' and resid 672 through 713 removed outlier: 3.541A pdb=" N LEU F 678 " --> pdb=" O ILE F 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS F 679 " --> pdb=" O ASP F 676 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 680 " --> pdb=" O ALA F 677 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR F 689 " --> pdb=" O HIS F 686 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER F 690 " --> pdb=" O ARG F 687 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 692 " --> pdb=" O TYR F 689 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 693 " --> pdb=" O SER F 690 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 695 " --> pdb=" O VAL F 692 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE F 696 " --> pdb=" O VAL F 693 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU F 703 " --> pdb=" O LEU F 700 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 705 " --> pdb=" O LEU F 702 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU F 706 " --> pdb=" O GLU F 703 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 708 " --> pdb=" O PHE F 705 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 710 " --> pdb=" O GLY F 707 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE F 712 " --> pdb=" O TRP F 709 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 713 " --> pdb=" O ILE F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 736 removed outlier: 3.552A pdb=" N VAL F 723 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE F 724 " --> pdb=" O ASP F 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 733 " --> pdb=" O ALA F 729 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA F 735 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE F 736 " --> pdb=" O ALA F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 776 Processing helix chain 'F' and resid 791 through 810 removed outlier: 3.580A pdb=" N MET F 795 " --> pdb=" O MET F 791 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 806 " --> pdb=" O THR F 802 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE F 807 " --> pdb=" O GLU F 803 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE F 808 " --> pdb=" O ASN F 804 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE F 809 " --> pdb=" O TRP F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 842 removed outlier: 3.732A pdb=" N THR F 840 " --> pdb=" O ALA F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 852 through 877 Processing helix chain 'F' and resid 880 through 887 Processing sheet with id= A, first strand: chain 'A' and resid 179 through 184 Processing sheet with id= B, first strand: chain 'A' and resid 201 through 204 Processing sheet with id= C, first strand: chain 'A' and resid 237 through 239 removed outlier: 3.594A pdb=" N ILE A 225 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 251 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 358 through 360 Processing sheet with id= E, first strand: chain 'A' and resid 553 through 556 removed outlier: 6.768A pdb=" N THR A 647 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY A 633 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 649 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 457 through 464 removed outlier: 3.611A pdb=" N ALA A 516 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY A 606 " --> pdb=" O TYR A 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 179 through 184 Processing sheet with id= I, first strand: chain 'B' and resid 201 through 204 Processing sheet with id= J, first strand: chain 'B' and resid 237 through 239 removed outlier: 3.593A pdb=" N ILE B 225 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 251 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 358 through 360 Processing sheet with id= L, first strand: chain 'B' and resid 553 through 556 removed outlier: 6.768A pdb=" N THR B 647 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY B 633 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE B 649 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 457 through 464 removed outlier: 3.611A pdb=" N ALA B 516 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY B 606 " --> pdb=" O TYR B 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 179 through 184 Processing sheet with id= P, first strand: chain 'C' and resid 201 through 204 Processing sheet with id= Q, first strand: chain 'C' and resid 237 through 239 removed outlier: 3.594A pdb=" N ILE C 225 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP C 226 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL C 251 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 358 through 360 Processing sheet with id= S, first strand: chain 'C' and resid 553 through 556 removed outlier: 6.769A pdb=" N THR C 647 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY C 633 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 649 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 457 through 464 removed outlier: 3.611A pdb=" N ALA C 516 " --> pdb=" O VAL C 473 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY C 606 " --> pdb=" O TYR C 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 179 through 184 Processing sheet with id= W, first strand: chain 'D' and resid 201 through 204 Processing sheet with id= X, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.593A pdb=" N ILE D 225 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP D 226 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL D 251 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 358 through 360 Processing sheet with id= Z, first strand: chain 'D' and resid 553 through 556 removed outlier: 6.769A pdb=" N THR D 647 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY D 633 " --> pdb=" O THR D 647 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 649 " --> pdb=" O GLY D 633 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 457 through 464 removed outlier: 3.612A pdb=" N ALA D 516 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY D 606 " --> pdb=" O TYR D 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 179 through 184 Processing sheet with id= AD, first strand: chain 'E' and resid 201 through 204 Processing sheet with id= AE, first strand: chain 'E' and resid 237 through 239 removed outlier: 3.594A pdb=" N ILE E 225 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP E 226 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL E 251 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 358 through 360 Processing sheet with id= AG, first strand: chain 'E' and resid 553 through 556 removed outlier: 6.768A pdb=" N THR E 647 " --> pdb=" O MET E 631 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY E 633 " --> pdb=" O THR E 647 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE E 649 " --> pdb=" O GLY E 633 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 457 through 464 removed outlier: 3.612A pdb=" N ALA E 516 " --> pdb=" O VAL E 473 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY E 606 " --> pdb=" O TYR E 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 179 through 184 Processing sheet with id= AK, first strand: chain 'F' and resid 201 through 204 Processing sheet with id= AL, first strand: chain 'F' and resid 237 through 239 removed outlier: 3.593A pdb=" N ILE F 225 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP F 226 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL F 251 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 358 through 360 Processing sheet with id= AN, first strand: chain 'F' and resid 553 through 556 removed outlier: 6.768A pdb=" N THR F 647 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLY F 633 " --> pdb=" O THR F 647 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE F 649 " --> pdb=" O GLY F 633 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'F' and resid 457 through 464 removed outlier: 3.611A pdb=" N ALA F 516 " --> pdb=" O VAL F 473 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'F' and resid 578 through 580 removed outlier: 6.949A pdb=" N GLY F 606 " --> pdb=" O TYR F 579 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP 1806 hydrogen bonds defined for protein. 4788 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: 14.30 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5940 1.27 - 1.40: 8562 1.40 - 1.54: 22118 1.54 - 1.68: 1912 1.68 - 1.81: 327 Bond restraints: 38859 Sorted by residual: bond pdb=" CG PRO B 198 " pdb=" CD PRO B 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO F 198 " pdb=" CD PRO F 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO D 198 " pdb=" CD PRO D 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 1.503 1.133 0.370 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO A 198 " pdb=" CD PRO A 198 " ideal model delta sigma weight residual 1.503 1.133 0.370 3.40e-02 8.65e+02 1.19e+02 ... (remaining 38854 not shown) Histogram of bond angle deviations from ideal: 83.96 - 94.02: 12 94.02 - 104.08: 500 104.08 - 114.15: 24336 114.15 - 124.21: 26548 124.21 - 134.27: 831 Bond angle restraints: 52227 Sorted by residual: angle pdb=" N PRO C 198 " pdb=" CD PRO C 198 " pdb=" CG PRO C 198 " ideal model delta sigma weight residual 103.20 83.96 19.24 1.50e+00 4.44e-01 1.65e+02 angle pdb=" N PRO A 198 " pdb=" CD PRO A 198 " pdb=" CG PRO A 198 " ideal model delta sigma weight residual 103.20 83.97 19.23 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO F 198 " pdb=" CD PRO F 198 " pdb=" CG PRO F 198 " ideal model delta sigma weight residual 103.20 83.98 19.22 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO E 198 " pdb=" CD PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 103.20 83.99 19.21 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO B 198 " pdb=" CD PRO B 198 " pdb=" CG PRO B 198 " ideal model delta sigma weight residual 103.20 83.99 19.21 1.50e+00 4.44e-01 1.64e+02 ... (remaining 52222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 20617 21.68 - 43.36: 2211 43.36 - 65.05: 543 65.05 - 86.73: 145 86.73 - 108.41: 43 Dihedral angle restraints: 23559 sinusoidal: 10479 harmonic: 13080 Sorted by residual: dihedral pdb=" CA GLU E 847 " pdb=" C GLU E 847 " pdb=" N ASN E 848 " pdb=" CA ASN E 848 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLU A 847 " pdb=" C GLU A 847 " pdb=" N ASN A 848 " pdb=" CA ASN A 848 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLU D 847 " pdb=" C GLU D 847 " pdb=" N ASN D 848 " pdb=" CA ASN D 848 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 23556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4246 0.054 - 0.108: 1263 0.108 - 0.163: 268 0.163 - 0.217: 34 0.217 - 0.271: 12 Chirality restraints: 5823 Sorted by residual: chirality pdb=" CA ASN E 386 " pdb=" N ASN E 386 " pdb=" C ASN E 386 " pdb=" CB ASN E 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN F 386 " pdb=" N ASN F 386 " pdb=" C ASN F 386 " pdb=" CB ASN F 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ASN B 386 " pdb=" N ASN B 386 " pdb=" C ASN B 386 " pdb=" CB ASN B 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5820 not shown) Planarity restraints: 6309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO B 211 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO F 211 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO F 211 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO F 211 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO C 211 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " -0.081 5.00e-02 4.00e+02 ... (remaining 6306 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 329 2.51 - 3.11: 27583 3.11 - 3.70: 59119 3.70 - 4.30: 86718 4.30 - 4.90: 142728 Nonbonded interactions: 316477 Sorted by model distance: nonbonded pdb=" O PHE E 313 " pdb=" O GLY F 783 " model vdw 1.910 3.040 nonbonded pdb=" O GLY A 783 " pdb=" O PHE F 313 " model vdw 1.972 3.040 nonbonded pdb=" O PHE C 313 " pdb=" O GLY D 783 " model vdw 1.993 3.040 nonbonded pdb=" O PHE B 313 " pdb=" O GLY C 783 " model vdw 2.011 3.040 nonbonded pdb=" OD1 ASP E 634 " pdb=" F3 BEF E1001 " model vdw 2.032 2.390 ... (remaining 316472 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 110 through 888 or resid 1001 through 1010)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 110 through 888 or resid 1001 through 1010)) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.510 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 94.010 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 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 : 0.013 0.371 38859 Z= 0.762 Angle : 1.591 19.243 52227 Z= 0.671 Chirality : 0.054 0.271 5823 Planarity : 0.008 0.161 6309 Dihedral : 19.286 108.411 15171 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.72 % Allowed : 0.54 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.11), residues: 4560 helix: -0.60 (0.09), residues: 2322 sheet: -0.21 (0.24), residues: 414 loop : -0.97 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 805 HIS 0.005 0.002 HIS E 614 PHE 0.032 0.002 PHE B 126 TYR 0.020 0.003 TYR D 691 ARG 0.009 0.001 ARG F 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 933 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.9015 (tt) cc_final: 0.8770 (tp) REVERT: B 154 ASN cc_start: 0.6397 (t0) cc_final: 0.6000 (m-40) REVERT: B 721 LEU cc_start: 0.7880 (mp) cc_final: 0.7554 (mp) REVERT: B 733 THR cc_start: 0.7382 (p) cc_final: 0.7051 (t) REVERT: B 802 THR cc_start: 0.8408 (p) cc_final: 0.8161 (p) REVERT: C 543 THR cc_start: 0.8149 (m) cc_final: 0.7794 (p) REVERT: D 405 MET cc_start: 0.0848 (ttp) cc_final: 0.0396 (ptp) REVERT: E 786 GLN cc_start: 0.5460 (tt0) cc_final: 0.5222 (tt0) REVERT: F 228 SER cc_start: 0.7399 (m) cc_final: 0.6990 (t) REVERT: F 848 ASN cc_start: 0.4236 (p0) cc_final: 0.4008 (t0) outliers start: 27 outliers final: 4 residues processed: 958 average time/residue: 0.4806 time to fit residues: 757.6877 Evaluate side-chains 447 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 443 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain E residue 400 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 266 optimal weight: 8.9990 chunk 414 optimal weight: 6.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN ** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 HIS B 542 GLN ** B 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 391 HIS C 432 GLN C 571 GLN C 751 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 686 HIS ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN E 686 HIS ** E 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 740 ASN E 792 ASN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN F 549 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 38859 Z= 0.570 Angle : 0.972 15.503 52227 Z= 0.480 Chirality : 0.052 0.244 5823 Planarity : 0.007 0.090 6309 Dihedral : 20.094 102.875 7316 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.18 % Allowed : 13.85 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 4560 helix: -0.11 (0.09), residues: 2442 sheet: -0.40 (0.21), residues: 468 loop : -1.29 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP F 805 HIS 0.013 0.003 HIS B 614 PHE 0.036 0.003 PHE D 808 TYR 0.040 0.003 TYR D 314 ARG 0.012 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 448 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.8988 (tt) cc_final: 0.8705 (tp) REVERT: A 766 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8177 (mp) REVERT: A 884 ARG cc_start: 0.6932 (tmt170) cc_final: 0.6277 (tmt170) REVERT: B 128 MET cc_start: 0.7579 (mmt) cc_final: 0.7346 (mmm) REVERT: B 159 PHE cc_start: 0.7765 (t80) cc_final: 0.7342 (t80) REVERT: C 127 VAL cc_start: 0.9220 (m) cc_final: 0.9011 (t) REVERT: C 187 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6710 (tm-30) REVERT: C 306 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8446 (mp) REVERT: C 391 HIS cc_start: 0.3065 (OUTLIER) cc_final: 0.2365 (m170) REVERT: C 405 MET cc_start: 0.2799 (ttt) cc_final: 0.2461 (ttt) REVERT: C 884 ARG cc_start: 0.6321 (tmt170) cc_final: 0.5978 (ptt-90) REVERT: D 258 MET cc_start: 0.2999 (ppp) cc_final: 0.2107 (ppp) REVERT: D 268 PHE cc_start: 0.0206 (OUTLIER) cc_final: -0.0473 (m-80) REVERT: D 845 TRP cc_start: 0.4414 (m100) cc_final: 0.4181 (m100) REVERT: E 285 HIS cc_start: 0.6603 (OUTLIER) cc_final: 0.6183 (t70) REVERT: E 582 GLU cc_start: 0.5453 (mm-30) cc_final: 0.4682 (mt-10) REVERT: E 614 HIS cc_start: 0.4781 (m170) cc_final: 0.4452 (m-70) REVERT: E 698 LEU cc_start: 0.8307 (mt) cc_final: 0.7171 (mt) REVERT: F 359 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7527 (tp) REVERT: F 631 MET cc_start: 0.6851 (ppp) cc_final: 0.6634 (ppp) REVERT: F 809 ILE cc_start: 0.8867 (mt) cc_final: 0.8662 (mt) REVERT: F 848 ASN cc_start: 0.5623 (p0) cc_final: 0.5149 (t0) outliers start: 156 outliers final: 89 residues processed: 569 average time/residue: 0.4547 time to fit residues: 440.5402 Evaluate side-chains 442 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 347 time to evaluate : 4.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 552 LEU Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 787 ASN Chi-restraints excluded: chain E residue 850 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 359 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 HIS Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 723 VAL Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 837 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 344 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 448 optimal weight: 0.9980 chunk 369 optimal weight: 1.9990 chunk 411 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 chunk 332 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN B 792 ASN C 391 HIS ** C 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 792 ASN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38859 Z= 0.196 Angle : 0.617 9.727 52227 Z= 0.312 Chirality : 0.042 0.209 5823 Planarity : 0.004 0.056 6309 Dihedral : 17.978 94.758 7312 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.16 % Allowed : 17.28 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 4560 helix: 0.43 (0.10), residues: 2436 sheet: -0.74 (0.20), residues: 570 loop : -1.23 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 805 HIS 0.014 0.001 HIS C 391 PHE 0.041 0.001 PHE E 830 TYR 0.024 0.001 TYR F 694 ARG 0.008 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 439 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 HIS cc_start: 0.5218 (OUTLIER) cc_final: 0.3354 (t-90) REVERT: A 546 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5937 (pm20) REVERT: A 700 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 722 ILE cc_start: 0.7970 (mm) cc_final: 0.7695 (mm) REVERT: A 758 MET cc_start: 0.7421 (mtm) cc_final: 0.7157 (mtm) REVERT: B 248 SER cc_start: 0.7155 (m) cc_final: 0.6798 (t) REVERT: C 127 VAL cc_start: 0.9055 (m) cc_final: 0.8708 (t) REVERT: C 187 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6570 (tm-30) REVERT: C 798 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 253 ARG cc_start: 0.6573 (OUTLIER) cc_final: 0.5908 (mtm110) REVERT: D 258 MET cc_start: 0.3157 (ppp) cc_final: 0.1984 (ppp) REVERT: D 268 PHE cc_start: 0.0232 (OUTLIER) cc_final: -0.0563 (m-10) REVERT: D 486 GLU cc_start: 0.5733 (pm20) cc_final: 0.4993 (pm20) REVERT: D 631 MET cc_start: 0.6710 (tpp) cc_final: 0.6263 (tpt) REVERT: E 152 MET cc_start: 0.3516 (mtt) cc_final: 0.3295 (mtt) REVERT: E 582 GLU cc_start: 0.5541 (mm-30) cc_final: 0.4700 (mt-10) REVERT: F 848 ASN cc_start: 0.5391 (p0) cc_final: 0.5189 (t0) REVERT: F 874 TYR cc_start: 0.7069 (t80) cc_final: 0.6725 (t80) outliers start: 118 outliers final: 62 residues processed: 525 average time/residue: 0.4359 time to fit residues: 391.7513 Evaluate side-chains 432 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 365 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 785 ILE Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 40.0000 chunk 311 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 416 optimal weight: 7.9990 chunk 440 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 chunk 394 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 500 ASN ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN C 357 GLN C 701 HIS ** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 ASN E 523 HIS ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 38859 Z= 0.388 Angle : 0.749 9.307 52227 Z= 0.372 Chirality : 0.046 0.202 5823 Planarity : 0.005 0.061 6309 Dihedral : 18.448 103.059 7312 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.01 % Allowed : 18.60 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 4560 helix: 0.23 (0.10), residues: 2424 sheet: -0.76 (0.20), residues: 582 loop : -1.27 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 756 HIS 0.020 0.002 HIS A 549 PHE 0.025 0.002 PHE E 286 TYR 0.032 0.002 TYR F 694 ARG 0.005 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 377 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5702 (mm) REVERT: A 700 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8780 (tp) REVERT: A 758 MET cc_start: 0.7604 (mtm) cc_final: 0.7347 (mtm) REVERT: A 884 ARG cc_start: 0.7052 (tmt170) cc_final: 0.6295 (tmt170) REVERT: B 159 PHE cc_start: 0.7673 (t80) cc_final: 0.7307 (t80) REVERT: B 248 SER cc_start: 0.7377 (m) cc_final: 0.7008 (t) REVERT: B 346 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7229 (mmt) REVERT: B 712 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (mp) REVERT: B 840 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8207 (m) REVERT: C 127 VAL cc_start: 0.9124 (m) cc_final: 0.8851 (t) REVERT: C 306 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 631 MET cc_start: 0.4881 (tmm) cc_final: 0.4394 (tmm) REVERT: D 253 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5996 (mtm110) REVERT: D 268 PHE cc_start: 0.0488 (OUTLIER) cc_final: -0.0731 (m-80) REVERT: D 486 GLU cc_start: 0.5573 (pm20) cc_final: 0.4724 (pm20) REVERT: D 609 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5311 (tt0) REVERT: E 118 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6282 (ttp) REVERT: E 430 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.5358 (mm) REVERT: E 582 GLU cc_start: 0.5560 (mm-30) cc_final: 0.4768 (mt-10) REVERT: F 271 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5524 (mmp-170) REVERT: F 848 ASN cc_start: 0.6097 (p0) cc_final: 0.5788 (t0) REVERT: F 860 ILE cc_start: 0.9203 (pt) cc_final: 0.8917 (pt) REVERT: F 874 TYR cc_start: 0.7110 (t80) cc_final: 0.6747 (t80) outliers start: 187 outliers final: 113 residues processed: 523 average time/residue: 0.4509 time to fit residues: 408.3480 Evaluate side-chains 461 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 336 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 803 GLU Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 875 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 835 ILE Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 497 ASN Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 787 ASN Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 850 THR Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 chunk 328 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 395 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN C 740 ASN D 391 HIS ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 ASN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 38859 Z= 0.345 Angle : 0.706 10.482 52227 Z= 0.351 Chirality : 0.045 0.288 5823 Planarity : 0.004 0.055 6309 Dihedral : 17.990 100.802 7312 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.14 % Allowed : 20.26 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4560 helix: 0.25 (0.10), residues: 2430 sheet: -0.80 (0.20), residues: 582 loop : -1.34 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 805 HIS 0.007 0.001 HIS F 391 PHE 0.043 0.002 PHE E 830 TYR 0.023 0.002 TYR B 694 ARG 0.011 0.001 ARG F 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 376 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 HIS cc_start: 0.4185 (OUTLIER) cc_final: 0.3752 (m90) REVERT: A 546 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: A 694 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8492 (t80) REVERT: A 700 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 758 MET cc_start: 0.7584 (mtm) cc_final: 0.7364 (mtm) REVERT: A 884 ARG cc_start: 0.7053 (tmt170) cc_final: 0.6335 (tmt170) REVERT: B 248 SER cc_start: 0.7402 (m) cc_final: 0.7079 (t) REVERT: B 346 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7119 (mmm) REVERT: C 127 VAL cc_start: 0.9184 (m) cc_final: 0.8828 (t) REVERT: C 150 LEU cc_start: 0.6535 (tp) cc_final: 0.6202 (tp) REVERT: D 118 MET cc_start: 0.4173 (mtp) cc_final: 0.3835 (mtp) REVERT: D 152 MET cc_start: 0.6111 (tpp) cc_final: 0.5864 (ttm) REVERT: D 253 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6123 (mtm110) REVERT: D 268 PHE cc_start: 0.0019 (OUTLIER) cc_final: -0.1225 (m-80) REVERT: D 397 GLU cc_start: 0.5055 (pm20) cc_final: 0.4855 (tt0) REVERT: D 486 GLU cc_start: 0.5795 (pm20) cc_final: 0.5066 (pm20) REVERT: D 530 MET cc_start: 0.3371 (mmp) cc_final: 0.3072 (mmm) REVERT: D 550 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6760 (mp) REVERT: D 609 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.5418 (tt0) REVERT: D 766 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (mm) REVERT: E 134 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7571 (tt) REVERT: F 258 MET cc_start: 0.5506 (mpp) cc_final: 0.4684 (ttp) REVERT: F 271 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5364 (mmp-170) REVERT: F 848 ASN cc_start: 0.6327 (p0) cc_final: 0.5891 (t0) REVERT: F 874 TYR cc_start: 0.7150 (t80) cc_final: 0.6803 (t80) outliers start: 192 outliers final: 120 residues processed: 523 average time/residue: 0.4405 time to fit residues: 394.3655 Evaluate side-chains 469 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 337 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 835 ILE Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 497 ASN Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 850 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 441 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 ASN B 792 ASN C 244 GLN C 432 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 391 HIS ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 887 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 GLN F 787 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 38859 Z= 0.469 Angle : 0.835 9.302 52227 Z= 0.414 Chirality : 0.049 0.255 5823 Planarity : 0.005 0.060 6309 Dihedral : 18.600 110.902 7312 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.03 % Allowed : 21.06 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 4560 helix: -0.19 (0.10), residues: 2430 sheet: -0.82 (0.21), residues: 528 loop : -1.53 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP F 805 HIS 0.009 0.002 HIS A 391 PHE 0.027 0.002 PHE E 286 TYR 0.029 0.003 TYR B 694 ARG 0.006 0.001 ARG E 583 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 364 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 PHE cc_start: 0.5707 (OUTLIER) cc_final: 0.5356 (m-10) REVERT: A 430 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5896 (mm) REVERT: A 700 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 758 MET cc_start: 0.7631 (mtm) cc_final: 0.7408 (mtm) REVERT: A 884 ARG cc_start: 0.7034 (tmt170) cc_final: 0.6727 (tmt170) REVERT: B 159 PHE cc_start: 0.7708 (t80) cc_final: 0.7389 (t80) REVERT: B 248 SER cc_start: 0.7593 (m) cc_final: 0.7331 (t) REVERT: B 367 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: C 127 VAL cc_start: 0.9250 (m) cc_final: 0.8891 (t) REVERT: C 150 LEU cc_start: 0.6809 (tp) cc_final: 0.6595 (tp) REVERT: C 346 MET cc_start: 0.6915 (mtm) cc_final: 0.6702 (mtm) REVERT: C 537 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6237 (mmm160) REVERT: C 819 SER cc_start: 0.7635 (m) cc_final: 0.7257 (t) REVERT: D 118 MET cc_start: 0.4103 (mtp) cc_final: 0.3770 (mtp) REVERT: D 253 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6191 (mtm110) REVERT: D 268 PHE cc_start: -0.0154 (OUTLIER) cc_final: -0.1274 (m-80) REVERT: D 353 LEU cc_start: 0.7183 (tp) cc_final: 0.6944 (tp) REVERT: D 530 MET cc_start: 0.3536 (mmp) cc_final: 0.3304 (mmm) REVERT: D 607 PHE cc_start: 0.6010 (OUTLIER) cc_final: 0.5041 (t80) REVERT: D 609 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.4985 (tm-30) REVERT: D 642 LEU cc_start: 0.5509 (mm) cc_final: 0.5283 (tp) REVERT: D 678 LEU cc_start: 0.7906 (tt) cc_final: 0.7559 (tp) REVERT: E 134 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7831 (tt) REVERT: E 258 MET cc_start: 0.3087 (OUTLIER) cc_final: 0.2421 (ppp) REVERT: E 884 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.6017 (ptt90) REVERT: F 258 MET cc_start: 0.5449 (mpp) cc_final: 0.4839 (ttp) REVERT: F 271 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.4884 (mmp-170) REVERT: F 847 GLU cc_start: 0.6391 (mp0) cc_final: 0.5642 (pt0) REVERT: F 874 TYR cc_start: 0.7217 (t80) cc_final: 0.6856 (t80) outliers start: 225 outliers final: 155 residues processed: 542 average time/residue: 0.4460 time to fit residues: 413.9124 Evaluate side-chains 495 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 327 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 840 THR Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 537 ARG Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 646 ASP Chi-restraints excluded: chain C residue 647 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 875 GLU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 607 PHE Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 791 MET Chi-restraints excluded: chain D residue 835 ILE Chi-restraints excluded: chain D residue 840 THR Chi-restraints excluded: chain D residue 846 SER Chi-restraints excluded: chain D residue 860 ILE Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 497 ASN Chi-restraints excluded: chain E residue 533 MET Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 752 LEU Chi-restraints excluded: chain E residue 787 ASN Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 837 THR Chi-restraints excluded: chain E residue 845 TRP Chi-restraints excluded: chain E residue 850 THR Chi-restraints excluded: chain E residue 884 ARG Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 257 PHE Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 647 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 730 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 371 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 439 optimal weight: 0.8980 chunk 275 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN C 285 HIS ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN F 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38859 Z= 0.182 Angle : 0.615 10.993 52227 Z= 0.309 Chirality : 0.042 0.289 5823 Planarity : 0.004 0.051 6309 Dihedral : 16.769 91.785 7312 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.70 % Allowed : 23.34 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4560 helix: 0.46 (0.10), residues: 2418 sheet: -0.90 (0.20), residues: 600 loop : -1.33 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 805 HIS 0.004 0.001 HIS B 495 PHE 0.038 0.001 PHE E 119 TYR 0.025 0.001 TYR F 694 ARG 0.007 0.000 ARG E 583 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 422 time to evaluate : 4.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.4819 (m-10) REVERT: A 538 ASP cc_start: 0.6085 (p0) cc_final: 0.5535 (m-30) REVERT: A 694 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.8373 (t80) REVERT: A 722 ILE cc_start: 0.7913 (mm) cc_final: 0.7422 (mm) REVERT: B 346 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: C 127 VAL cc_start: 0.9084 (m) cc_final: 0.8824 (t) REVERT: C 150 LEU cc_start: 0.6446 (tp) cc_final: 0.6201 (tp) REVERT: C 526 ILE cc_start: 0.3553 (mt) cc_final: 0.3289 (tp) REVERT: C 798 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 819 SER cc_start: 0.7526 (m) cc_final: 0.7277 (t) REVERT: C 880 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6972 (tm-30) REVERT: D 118 MET cc_start: 0.4153 (mtp) cc_final: 0.3801 (mtp) REVERT: D 253 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6115 (mtm110) REVERT: E 884 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6359 (ptt90) REVERT: F 258 MET cc_start: 0.5347 (mpp) cc_final: 0.4422 (ttp) REVERT: F 271 ARG cc_start: 0.6231 (OUTLIER) cc_final: 0.4803 (mmp-170) REVERT: F 731 VAL cc_start: 0.7229 (m) cc_final: 0.7018 (t) REVERT: F 847 GLU cc_start: 0.6122 (mp0) cc_final: 0.5769 (mt-10) REVERT: F 874 TYR cc_start: 0.6999 (t80) cc_final: 0.6651 (t80) outliers start: 138 outliers final: 79 residues processed: 521 average time/residue: 0.4320 time to fit residues: 388.4579 Evaluate side-chains 448 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 363 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 884 ARG Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 758 MET Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 853 VAL Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 701 HIS ** E 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38859 Z= 0.203 Angle : 0.630 17.899 52227 Z= 0.313 Chirality : 0.043 0.496 5823 Planarity : 0.004 0.050 6309 Dihedral : 16.315 95.257 7312 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.32 % Allowed : 24.68 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4560 helix: 0.62 (0.10), residues: 2412 sheet: -0.86 (0.20), residues: 600 loop : -1.27 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 756 HIS 0.006 0.001 HIS D 686 PHE 0.051 0.001 PHE E 830 TYR 0.027 0.001 TYR F 694 ARG 0.006 0.000 ARG E 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 404 time to evaluate : 4.282 Fit side-chains revert: symmetry clash REVERT: A 268 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.4785 (m-10) REVERT: A 530 MET cc_start: 0.5242 (mmm) cc_final: 0.4430 (mmt) REVERT: A 538 ASP cc_start: 0.5951 (p0) cc_final: 0.5319 (m-30) REVERT: B 346 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6987 (mmt) REVERT: B 367 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5757 (tm-30) REVERT: B 405 MET cc_start: 0.7095 (tpp) cc_final: 0.6769 (tpt) REVERT: C 127 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8725 (t) REVERT: C 346 MET cc_start: 0.7058 (mtm) cc_final: 0.6710 (mtm) REVERT: C 819 SER cc_start: 0.7552 (m) cc_final: 0.7302 (t) REVERT: D 118 MET cc_start: 0.4035 (mtp) cc_final: 0.3709 (mtp) REVERT: D 268 PHE cc_start: -0.0217 (OUTLIER) cc_final: -0.1519 (m-10) REVERT: E 884 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6032 (ptt90) REVERT: F 129 GLU cc_start: 0.7994 (mp0) cc_final: 0.7592 (mp0) REVERT: F 258 MET cc_start: 0.5391 (mpp) cc_final: 0.4422 (ttp) REVERT: F 271 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.4831 (mmp-170) REVERT: F 731 VAL cc_start: 0.7142 (m) cc_final: 0.6801 (t) REVERT: F 847 GLU cc_start: 0.6138 (mp0) cc_final: 0.5605 (mt-10) REVERT: F 874 TYR cc_start: 0.6915 (t80) cc_final: 0.6582 (t80) outliers start: 124 outliers final: 88 residues processed: 493 average time/residue: 0.4153 time to fit residues: 353.2635 Evaluate side-chains 464 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 369 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 385 LYS Chi-restraints excluded: chain E residue 405 MET Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 690 SER Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 849 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 884 ARG Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 253 ARG Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 0.7980 chunk 421 optimal weight: 0.0570 chunk 384 optimal weight: 5.9990 chunk 409 optimal weight: 8.9990 chunk 420 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 370 optimal weight: 0.3980 chunk 387 optimal weight: 9.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 701 HIS F 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 38859 Z= 0.170 Angle : 0.611 16.831 52227 Z= 0.305 Chirality : 0.043 0.453 5823 Planarity : 0.004 0.048 6309 Dihedral : 15.419 89.797 7312 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.87 % Allowed : 25.19 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4560 helix: 0.74 (0.10), residues: 2370 sheet: -0.59 (0.21), residues: 534 loop : -1.25 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 845 HIS 0.005 0.001 HIS B 240 PHE 0.021 0.001 PHE A 611 TYR 0.022 0.001 TYR F 694 ARG 0.007 0.000 ARG E 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 417 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.4679 (m-10) REVERT: A 530 MET cc_start: 0.5305 (mmm) cc_final: 0.4382 (mmt) REVERT: A 538 ASP cc_start: 0.5928 (p0) cc_final: 0.5543 (m-30) REVERT: A 696 ILE cc_start: 0.8201 (pt) cc_final: 0.7817 (pt) REVERT: A 722 ILE cc_start: 0.7778 (mm) cc_final: 0.7530 (mm) REVERT: B 346 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6924 (mmt) REVERT: B 367 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5602 (tm-30) REVERT: B 405 MET cc_start: 0.7038 (tpp) cc_final: 0.6744 (tpt) REVERT: C 230 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7113 (mp) REVERT: C 258 MET cc_start: 0.4698 (mpp) cc_final: 0.4426 (mpp) REVERT: C 346 MET cc_start: 0.7029 (mtm) cc_final: 0.6785 (mtm) REVERT: C 819 SER cc_start: 0.7510 (m) cc_final: 0.7294 (t) REVERT: D 253 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6303 (mtm110) REVERT: D 268 PHE cc_start: -0.0424 (OUTLIER) cc_final: -0.1441 (m-10) REVERT: D 314 TYR cc_start: 0.8149 (m-80) cc_final: 0.7909 (m-80) REVERT: D 533 MET cc_start: 0.0054 (ptm) cc_final: -0.0600 (ptm) REVERT: D 678 LEU cc_start: 0.7714 (tt) cc_final: 0.7392 (tp) REVERT: E 583 ARG cc_start: 0.6073 (ttt90) cc_final: 0.5693 (mmp80) REVERT: E 884 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6134 (ptt90) REVERT: E 886 MET cc_start: 0.5789 (tpp) cc_final: 0.5009 (mmp) REVERT: F 258 MET cc_start: 0.5390 (mpp) cc_final: 0.4305 (ttp) REVERT: F 271 ARG cc_start: 0.6353 (OUTLIER) cc_final: 0.4840 (mmp-170) REVERT: F 731 VAL cc_start: 0.6992 (m) cc_final: 0.6678 (t) REVERT: F 874 TYR cc_start: 0.6775 (t80) cc_final: 0.6550 (t80) outliers start: 107 outliers final: 78 residues processed: 494 average time/residue: 0.4445 time to fit residues: 377.2795 Evaluate side-chains 465 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 379 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 385 LYS Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 849 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 884 ARG Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 628 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 5.9990 chunk 268 optimal weight: 8.9990 chunk 433 optimal weight: 7.9990 chunk 264 optimal weight: 0.3980 chunk 205 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 454 optimal weight: 1.9990 chunk 418 optimal weight: 0.0980 chunk 361 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 38859 Z= 0.222 Angle : 0.637 15.521 52227 Z= 0.316 Chirality : 0.044 0.414 5823 Planarity : 0.004 0.049 6309 Dihedral : 15.678 96.865 7312 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.89 % Allowed : 25.29 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.12), residues: 4560 helix: 0.78 (0.11), residues: 2352 sheet: -0.54 (0.21), residues: 546 loop : -1.14 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 805 HIS 0.005 0.001 HIS A 391 PHE 0.023 0.001 PHE B 222 TYR 0.020 0.001 TYR A 694 ARG 0.007 0.000 ARG F 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 379 time to evaluate : 3.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.4786 (m-10) REVERT: A 530 MET cc_start: 0.5301 (mmm) cc_final: 0.4454 (mmt) REVERT: A 538 ASP cc_start: 0.5885 (p0) cc_final: 0.5426 (m-30) REVERT: A 696 ILE cc_start: 0.8324 (pt) cc_final: 0.8120 (pt) REVERT: B 346 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6950 (mmt) REVERT: B 405 MET cc_start: 0.6998 (tpp) cc_final: 0.6693 (tpt) REVERT: C 346 MET cc_start: 0.7006 (mtm) cc_final: 0.6783 (mtm) REVERT: C 405 MET cc_start: 0.1884 (ttt) cc_final: 0.0741 (tpt) REVERT: C 819 SER cc_start: 0.7543 (m) cc_final: 0.7298 (t) REVERT: D 253 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6274 (mtm110) REVERT: D 268 PHE cc_start: -0.0247 (OUTLIER) cc_final: -0.1422 (m-10) REVERT: D 533 MET cc_start: -0.0020 (ptm) cc_final: -0.0624 (ttm) REVERT: D 535 PRO cc_start: 0.4332 (Cg_endo) cc_final: 0.3912 (Cg_exo) REVERT: D 678 LEU cc_start: 0.7763 (tt) cc_final: 0.7459 (tp) REVERT: D 696 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8037 (pt) REVERT: E 698 LEU cc_start: 0.7900 (mt) cc_final: 0.7627 (mt) REVERT: E 884 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.6156 (ptt90) REVERT: E 886 MET cc_start: 0.6079 (tpp) cc_final: 0.5059 (mmp) REVERT: F 258 MET cc_start: 0.5446 (mpp) cc_final: 0.4433 (ttp) REVERT: F 271 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.4939 (mmp-170) REVERT: F 731 VAL cc_start: 0.7032 (m) cc_final: 0.6691 (t) REVERT: F 874 TYR cc_start: 0.6803 (t80) cc_final: 0.6600 (t80) outliers start: 108 outliers final: 87 residues processed: 461 average time/residue: 0.4405 time to fit residues: 352.0423 Evaluate side-chains 461 residues out of total 3732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 367 time to evaluate : 3.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 744 SER Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 810 THR Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 703 GLU Chi-restraints excluded: chain D residue 759 SER Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 385 LYS Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 665 VAL Chi-restraints excluded: chain E residue 750 TRP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 849 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain E residue 884 ARG Chi-restraints excluded: chain F residue 120 PHE Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 271 ARG Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain F residue 703 GLU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 385 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 362 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 372 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 ASN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.146174 restraints weight = 60271.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.138568 restraints weight = 36455.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.137520 restraints weight = 70439.215| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 38859 Z= 0.180 Angle : 0.615 16.174 52227 Z= 0.306 Chirality : 0.043 0.584 5823 Planarity : 0.004 0.047 6309 Dihedral : 15.100 94.771 7312 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.89 % Allowed : 25.40 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.12), residues: 4560 helix: 0.76 (0.11), residues: 2370 sheet: -0.48 (0.22), residues: 510 loop : -1.23 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 845 HIS 0.005 0.001 HIS D 686 PHE 0.035 0.001 PHE E 126 TYR 0.020 0.001 TYR D 694 ARG 0.006 0.000 ARG F 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7746.48 seconds wall clock time: 142 minutes 34.21 seconds (8554.21 seconds total)