Starting phenix.real_space_refine on Fri Apr 12 03:45:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2024/7eot_31230_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2024/7eot_31230.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/7eot_31230/04_2024/7eot_31230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2024/7eot_31230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2024/7eot_31230_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2024/7eot_31230_trim_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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 P 2 5.49 5 S 150 5.16 5 C 15758 2.51 5 N 4120 2.21 5 O 4566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24598 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5980 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6186 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 32, 'TRANS': 754} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5980 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 6186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6186 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 32, 'TRANS': 754} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 119 Unusual residues: {'J86': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 119 Unusual residues: {'J86': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 12.85, per 1000 atoms: 0.52 Number of scatterers: 24598 At special positions: 0 Unit cell: (118.8, 143.64, 185.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 150 16.00 P 2 15.00 O 4566 8.00 N 4120 7.00 C 15758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 203 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 276 " " NAG B 905 " - " ASN B 368 " " NAG B 906 " - " ASN B 471 " " NAG B 907 " - " ASN B 771 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 203 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 276 " " NAG D 905 " - " ASN D 368 " " NAG D 906 " - " ASN D 471 " " NAG D 907 " - " ASN D 771 " Time building additional restraints: 9.48 Conformation dependent library (CDL) restraints added in 3.9 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 24 sheets defined 37.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 108 through 120 removed outlier: 3.689A pdb=" N PHE A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 removed outlier: 3.848A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.135A pdb=" N LYS A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.606A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 309 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.046A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.855A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 626 through 651 removed outlier: 4.467A pdb=" N VAL A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALA A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 671 No H-bonds generated for 'chain 'A' and resid 668 through 671' Processing helix chain 'A' and resid 673 through 675 No H-bonds generated for 'chain 'A' and resid 673 through 675' Processing helix chain 'A' and resid 689 through 697 Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.154A pdb=" N GLN A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 704 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 772 through 785 removed outlier: 3.817A pdb=" N ASP A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.688A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'B' and resid 36 through 51 removed outlier: 4.117A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.250A pdb=" N GLU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 258 through 261 No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 277 through 296 removed outlier: 4.130A pdb=" N GLY B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.355A pdb=" N TYR B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 581 removed outlier: 3.706A pdb=" N TRP B 563 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 573 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'B' and resid 627 through 656 removed outlier: 3.535A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 674 removed outlier: 3.527A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 670 through 674' Processing helix chain 'B' and resid 688 through 695 removed outlier: 3.562A pdb=" N ARG B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 708 removed outlier: 3.727A pdb=" N SER B 700 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR B 701 " --> pdb=" O CYS B 698 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET B 706 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 722 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.251A pdb=" N PHE B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 Processing helix chain 'B' and resid 784 through 792 Processing helix chain 'B' and resid 811 through 842 removed outlier: 4.240A pdb=" N VAL B 820 " --> pdb=" O VAL B 816 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 57 Proline residue: C 57 - end of helix Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 108 through 120 removed outlier: 3.599A pdb=" N PHE C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 165 removed outlier: 3.873A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.182A pdb=" N LYS C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.614A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 309 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 459 through 471 removed outlier: 3.515A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 500 Processing helix chain 'C' and resid 561 through 580 removed outlier: 3.872A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 611 Processing helix chain 'C' and resid 626 through 651 removed outlier: 4.511A pdb=" N VAL C 633 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TRP C 634 " --> pdb=" O MET C 630 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 671 No H-bonds generated for 'chain 'C' and resid 668 through 671' Processing helix chain 'C' and resid 673 through 675 No H-bonds generated for 'chain 'C' and resid 673 through 675' Processing helix chain 'C' and resid 689 through 695 removed outlier: 3.594A pdb=" N ASN C 693 " --> pdb=" O SER C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 4.144A pdb=" N GLN C 703 " --> pdb=" O PRO C 699 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 704 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 772 through 785 removed outlier: 3.833A pdb=" N ASP C 776 " --> pdb=" O LYS C 772 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 795 removed outlier: 3.711A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 836 Processing helix chain 'D' and resid 36 through 51 removed outlier: 4.094A pdb=" N LYS D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.217A pdb=" N GLU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 225 through 237 Processing helix chain 'D' and resid 258 through 261 No H-bonds generated for 'chain 'D' and resid 258 through 261' Processing helix chain 'D' and resid 277 through 296 removed outlier: 4.191A pdb=" N GLY D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.362A pdb=" N TYR D 526 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 581 removed outlier: 3.732A pdb=" N TRP D 563 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 573 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 614 Processing helix chain 'D' and resid 627 through 656 removed outlier: 3.564A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 674 removed outlier: 3.500A pdb=" N ASN D 674 " --> pdb=" O PRO D 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 670 through 674' Processing helix chain 'D' and resid 688 through 695 removed outlier: 3.596A pdb=" N ARG D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 708 removed outlier: 3.696A pdb=" N SER D 700 " --> pdb=" O VAL D 697 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR D 701 " --> pdb=" O CYS D 698 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET D 706 " --> pdb=" O TYR D 703 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU D 707 " --> pdb=" O ARG D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.307A pdb=" N PHE D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 781 Processing helix chain 'D' and resid 784 through 792 Processing helix chain 'D' and resid 811 through 842 removed outlier: 4.248A pdb=" N VAL D 820 " --> pdb=" O VAL D 816 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 68 through 73 removed outlier: 3.747A pdb=" N LEU A 72 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 40 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY A 97 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N MET A 39 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 99 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE A 100 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 125 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 204 through 206 removed outlier: 7.247A pdb=" N VAL A 173 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU A 228 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR A 175 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TYR A 230 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE A 254 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 229 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 256 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 277 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 276 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 366 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL A 365 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 374 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 406 through 410 removed outlier: 3.654A pdb=" N ASP A 476 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 435 through 441 removed outlier: 3.737A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 533 through 536 removed outlier: 3.509A pdb=" N TYR A 730 " --> pdb=" O SER A 534 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.817A pdb=" N GLY B 30 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 91 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL B 92 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 119 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.930A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 246 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU B 221 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 248 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 269 through 271 removed outlier: 3.573A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 399 through 402 removed outlier: 5.940A pdb=" N GLU B 475 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR B 402 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS B 477 " --> pdb=" O THR B 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 410 through 413 removed outlier: 3.520A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 512 through 515 removed outlier: 4.554A pdb=" N ALA B 515 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY B 759 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 728 through 731 removed outlier: 3.668A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 68 through 73 removed outlier: 3.794A pdb=" N LEU C 72 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 40 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY C 97 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET C 39 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL C 99 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE C 100 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 125 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 204 through 206 removed outlier: 7.470A pdb=" N VAL C 173 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU C 228 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR C 175 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR C 230 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE C 254 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C 229 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE C 256 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU C 276 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 366 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL C 365 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS C 374 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 406 through 410 removed outlier: 3.706A pdb=" N ASP C 476 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 434 through 439 removed outlier: 4.298A pdb=" N VAL C 434 " --> pdb=" O CYS C 456 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 533 through 537 Processing sheet with id= R, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.790A pdb=" N GLY D 30 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 91 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL D 92 " --> pdb=" O PRO D 117 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU D 119 " --> pdb=" O VAL D 92 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.743A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 222 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 246 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU D 221 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU D 248 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 269 through 271 removed outlier: 6.537A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 400 through 402 Processing sheet with id= V, first strand: chain 'D' and resid 409 through 413 removed outlier: 3.678A pdb=" N GLY D 438 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 513 through 515 removed outlier: 4.506A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.671A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2202 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.23 Time building geometry restraints manager: 10.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7932 1.36 - 1.49: 6505 1.49 - 1.62: 10461 1.62 - 1.76: 0 1.76 - 1.89: 260 Bond restraints: 25158 Sorted by residual: bond pdb=" N PRO B 516 " pdb=" CD PRO B 516 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.33e+01 bond pdb=" C1 J86 B 908 " pdb=" P1 J86 B 908 " ideal model delta sigma weight residual 1.887 1.798 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 J86 D 908 " pdb=" P1 J86 D 908 " ideal model delta sigma weight residual 1.887 1.798 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O2 J86 B 908 " pdb=" P1 J86 B 908 " ideal model delta sigma weight residual 1.533 1.620 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" O2 J86 D 908 " pdb=" P1 J86 D 908 " ideal model delta sigma weight residual 1.533 1.620 -0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 25153 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 743 106.74 - 113.57: 13887 113.57 - 120.40: 9084 120.40 - 127.23: 10105 127.23 - 134.06: 299 Bond angle restraints: 34118 Sorted by residual: angle pdb=" N LEU D 517 " pdb=" CA LEU D 517 " pdb=" C LEU D 517 " ideal model delta sigma weight residual 108.96 117.80 -8.84 1.59e+00 3.96e-01 3.09e+01 angle pdb=" N LEU B 517 " pdb=" CA LEU B 517 " pdb=" C LEU B 517 " ideal model delta sigma weight residual 108.41 116.83 -8.42 1.61e+00 3.86e-01 2.74e+01 angle pdb=" C1 J86 D 908 " pdb=" P1 J86 D 908 " pdb=" O3 J86 D 908 " ideal model delta sigma weight residual 102.38 115.01 -12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1 J86 B 908 " pdb=" P1 J86 B 908 " pdb=" O3 J86 B 908 " ideal model delta sigma weight residual 102.38 115.00 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1 J86 D 908 " pdb=" P1 J86 D 908 " pdb=" O2 J86 D 908 " ideal model delta sigma weight residual 114.24 103.00 11.24 3.00e+00 1.11e-01 1.40e+01 ... (remaining 34113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 13935 11.99 - 23.97: 835 23.97 - 35.96: 294 35.96 - 47.94: 95 47.94 - 59.93: 21 Dihedral angle restraints: 15180 sinusoidal: 6232 harmonic: 8948 Sorted by residual: dihedral pdb=" N SER D 688 " pdb=" C SER D 688 " pdb=" CA SER D 688 " pdb=" CB SER D 688 " ideal model delta harmonic sigma weight residual 122.80 111.13 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" N SER B 688 " pdb=" C SER B 688 " pdb=" CA SER B 688 " pdb=" CB SER B 688 " ideal model delta harmonic sigma weight residual 122.80 111.29 11.51 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" CA ASN B 491 " pdb=" C ASN B 491 " pdb=" N ASN B 492 " pdb=" CA ASN B 492 " ideal model delta harmonic sigma weight residual 180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 15177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3557 0.078 - 0.156: 321 0.156 - 0.234: 4 0.234 - 0.312: 2 0.312 - 0.390: 2 Chirality restraints: 3886 Sorted by residual: chirality pdb=" CA SER D 688 " pdb=" N SER D 688 " pdb=" C SER D 688 " pdb=" CB SER D 688 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA SER B 688 " pdb=" N SER B 688 " pdb=" C SER B 688 " pdb=" CB SER B 688 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA PRO B 516 " pdb=" N PRO B 516 " pdb=" C PRO B 516 " pdb=" CB PRO B 516 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3883 not shown) Planarity restraints: 4306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 515 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 516 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 516 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 516 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 326 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 327 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 326 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO C 327 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " 0.016 5.00e-02 4.00e+02 ... (remaining 4303 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 336 2.64 - 3.20: 22899 3.20 - 3.77: 38054 3.77 - 4.33: 49704 4.33 - 4.90: 80488 Nonbonded interactions: 191481 Sorted by model distance: nonbonded pdb=" CB LYS D 685 " pdb=" OE1 GLN D 686 " model vdw 2.074 3.440 nonbonded pdb=" N GLN D 686 " pdb=" OE1 GLN D 686 " model vdw 2.077 2.520 nonbonded pdb=" N GLN B 686 " pdb=" OE1 GLN B 686 " model vdw 2.078 2.520 nonbonded pdb=" CB LYS B 685 " pdb=" OE1 GLN B 686 " model vdw 2.097 3.440 nonbonded pdb=" O THR A 793 " pdb=" OG1 THR A 797 " model vdw 2.196 2.440 ... (remaining 191476 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.830 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: 0.020 Extract box with map and model: 5.310 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 63.050 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 25158 Z= 0.169 Angle : 0.523 12.630 34118 Z= 0.289 Chirality : 0.041 0.390 3886 Planarity : 0.003 0.035 4290 Dihedral : 9.380 59.930 9346 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.22 % Allowed : 6.06 % Favored : 91.72 % Cbeta Deviations : 0.07 % 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: 0.02 (0.16), residues: 3048 helix: 1.53 (0.16), residues: 1186 sheet: -1.12 (0.30), residues: 340 loop : -0.94 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 636 HIS 0.002 0.000 HIS B 134 PHE 0.009 0.001 PHE B 753 TYR 0.005 0.001 TYR C 180 ARG 0.002 0.000 ARG D 489 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 590 time to evaluate : 2.775 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7007 (mmp) cc_final: 0.6230 (tmm) REVERT: A 100 PHE cc_start: 0.8076 (t80) cc_final: 0.7807 (t80) REVERT: A 135 MET cc_start: 0.2040 (pmm) cc_final: 0.1801 (mmm) REVERT: A 145 PHE cc_start: 0.7004 (m-80) cc_final: 0.6678 (m-80) REVERT: A 162 MET cc_start: 0.7998 (mmm) cc_final: 0.7645 (mmt) REVERT: A 306 MET cc_start: 0.4479 (tmm) cc_final: 0.3622 (ttt) REVERT: A 419 VAL cc_start: 0.5969 (p) cc_final: 0.5468 (p) REVERT: A 434 VAL cc_start: 0.4835 (m) cc_final: 0.4051 (m) REVERT: A 606 TRP cc_start: 0.6506 (m100) cc_final: 0.6305 (m100) REVERT: A 609 TRP cc_start: 0.6801 (m100) cc_final: 0.6563 (m100) REVERT: B 39 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5931 (tt0) REVERT: B 153 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7839 (tp30) REVERT: B 163 ILE cc_start: 0.8036 (tp) cc_final: 0.7687 (tt) REVERT: B 249 VAL cc_start: 0.7900 (t) cc_final: 0.7436 (t) REVERT: B 298 LYS cc_start: 0.7538 (mmmm) cc_final: 0.7178 (mtmm) REVERT: B 520 ASN cc_start: 0.8229 (m-40) cc_final: 0.7993 (m110) REVERT: C 135 MET cc_start: 0.3917 (pmm) cc_final: 0.3378 (mmm) REVERT: C 145 PHE cc_start: 0.6687 (m-80) cc_final: 0.6024 (m-80) REVERT: C 162 MET cc_start: 0.8245 (mmm) cc_final: 0.7847 (mmt) REVERT: C 257 VAL cc_start: 0.7323 (t) cc_final: 0.6935 (m) REVERT: C 419 VAL cc_start: 0.6912 (OUTLIER) cc_final: 0.6675 (p) REVERT: C 475 TYR cc_start: 0.5901 (m-10) cc_final: 0.5481 (m-80) REVERT: C 606 TRP cc_start: 0.6808 (m100) cc_final: 0.6112 (m100) REVERT: C 649 LEU cc_start: 0.8182 (mm) cc_final: 0.7693 (mp) REVERT: D 41 MET cc_start: 0.8089 (ptp) cc_final: 0.6640 (ptt) REVERT: D 232 TYR cc_start: 0.5244 (t80) cc_final: 0.2541 (t80) REVERT: D 329 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7333 (mmtp) REVERT: D 341 ASN cc_start: 0.8857 (t0) cc_final: 0.8603 (m-40) REVERT: D 607 MET cc_start: 0.5784 (mpp) cc_final: 0.5282 (ptt) REVERT: D 703 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5426 (m-80) REVERT: D 762 MET cc_start: 0.5860 (mtm) cc_final: 0.5508 (mtm) outliers start: 59 outliers final: 13 residues processed: 640 average time/residue: 0.4118 time to fit residues: 399.4277 Evaluate side-chains 353 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 731 TRP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 703 TYR Chi-restraints excluded: chain D residue 730 ILE Chi-restraints excluded: chain D residue 731 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 79 optimal weight: 0.0060 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 145 optimal weight: 0.0670 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 overall best weight: 1.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 85 HIS ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS B 40 GLN B 48 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS B 780 HIS ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 449 HIS D 477 HIS ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25158 Z= 0.232 Angle : 0.584 9.761 34118 Z= 0.297 Chirality : 0.043 0.256 3886 Planarity : 0.004 0.072 4290 Dihedral : 5.169 58.172 3690 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.09 % Allowed : 12.65 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 3048 helix: 1.32 (0.15), residues: 1194 sheet: -1.10 (0.27), residues: 370 loop : -1.12 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 160 HIS 0.010 0.001 HIS B 293 PHE 0.024 0.002 PHE A 183 TYR 0.016 0.002 TYR A 700 ARG 0.015 0.001 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 343 time to evaluate : 3.033 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: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7037 (mmp) cc_final: 0.6496 (tmm) REVERT: A 47 THR cc_start: 0.5953 (OUTLIER) cc_final: 0.5656 (t) REVERT: A 74 MET cc_start: 0.7229 (tpp) cc_final: 0.7025 (tpp) REVERT: A 100 PHE cc_start: 0.8247 (t80) cc_final: 0.7930 (t80) REVERT: A 135 MET cc_start: 0.2573 (pmm) cc_final: 0.2331 (mmm) REVERT: A 177 PHE cc_start: 0.3158 (OUTLIER) cc_final: 0.2915 (m-10) REVERT: A 306 MET cc_start: 0.4470 (tmm) cc_final: 0.3641 (ttt) REVERT: A 475 TYR cc_start: 0.7079 (p90) cc_final: 0.6291 (m-10) REVERT: A 823 MET cc_start: 0.7780 (ptp) cc_final: 0.7016 (mmm) REVERT: B 74 MET cc_start: 0.4773 (ppp) cc_final: 0.4367 (ppp) REVERT: B 153 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8099 (tp30) REVERT: C 200 MET cc_start: 0.6918 (mmm) cc_final: 0.6702 (mmm) REVERT: C 606 TRP cc_start: 0.6879 (m100) cc_final: 0.6174 (m100) REVERT: C 609 TRP cc_start: 0.7501 (m100) cc_final: 0.7032 (m100) REVERT: D 323 ARG cc_start: 0.8830 (mmp80) cc_final: 0.8529 (mmt180) REVERT: D 329 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7460 (mmtp) REVERT: D 354 MET cc_start: 0.7217 (tpp) cc_final: 0.6942 (tpp) outliers start: 82 outliers final: 43 residues processed: 404 average time/residue: 0.3780 time to fit residues: 237.2708 Evaluate side-chains 312 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 267 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 674 ASN Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 688 SER Chi-restraints excluded: chain B residue 813 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 777 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 730 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 231 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 276 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS B 40 GLN ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 HIS B 782 ASN C 85 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 GLN D 48 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 782 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25158 Z= 0.155 Angle : 0.542 8.350 34118 Z= 0.274 Chirality : 0.042 0.210 3886 Planarity : 0.004 0.054 4290 Dihedral : 4.581 58.808 3680 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.90 % Allowed : 14.42 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 3048 helix: 1.06 (0.15), residues: 1194 sheet: -1.32 (0.27), residues: 376 loop : -1.10 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 606 HIS 0.009 0.001 HIS D 477 PHE 0.036 0.001 PHE A 183 TYR 0.024 0.001 TYR C 251 ARG 0.006 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 290 time to evaluate : 2.659 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: A 39 MET cc_start: 0.7018 (mmp) cc_final: 0.6453 (tmm) REVERT: A 177 PHE cc_start: 0.2988 (OUTLIER) cc_final: 0.2714 (m-10) REVERT: A 306 MET cc_start: 0.4591 (tmm) cc_final: 0.3816 (ttt) REVERT: A 331 MET cc_start: 0.5806 (tpp) cc_final: 0.5513 (tpp) REVERT: A 823 MET cc_start: 0.7757 (ptp) cc_final: 0.7032 (mmm) REVERT: B 153 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8143 (tp30) REVERT: B 163 ILE cc_start: 0.8535 (tp) cc_final: 0.8261 (tt) REVERT: B 354 MET cc_start: 0.7745 (tpp) cc_final: 0.7434 (tpp) REVERT: B 818 MET cc_start: 0.5075 (ppp) cc_final: 0.4859 (ppp) REVERT: C 135 MET cc_start: 0.4122 (pmm) cc_final: 0.3331 (ptm) REVERT: C 162 MET cc_start: 0.8421 (mmt) cc_final: 0.8090 (mmt) REVERT: C 606 TRP cc_start: 0.6917 (m100) cc_final: 0.6220 (m100) REVERT: C 609 TRP cc_start: 0.7550 (m100) cc_final: 0.7100 (m100) REVERT: C 783 VAL cc_start: 0.8739 (p) cc_final: 0.8538 (t) REVERT: C 823 MET cc_start: 0.5840 (ptp) cc_final: 0.5281 (mmm) REVERT: D 36 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8014 (mmm160) REVERT: D 41 MET cc_start: 0.7392 (ptp) cc_final: 0.5765 (ptt) REVERT: D 163 ILE cc_start: 0.8049 (tp) cc_final: 0.7633 (tt) REVERT: D 329 LYS cc_start: 0.7971 (tmtt) cc_final: 0.7557 (mmtp) REVERT: D 641 MET cc_start: 0.8753 (tpp) cc_final: 0.8499 (tpt) outliers start: 77 outliers final: 42 residues processed: 350 average time/residue: 0.3469 time to fit residues: 197.1354 Evaluate side-chains 303 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 766 GLN Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 677 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 279 optimal weight: 5.9990 chunk 295 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 147 GLN ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 780 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 782 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25158 Z= 0.248 Angle : 0.571 8.300 34118 Z= 0.291 Chirality : 0.043 0.206 3886 Planarity : 0.004 0.046 4290 Dihedral : 4.425 52.497 3676 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.46 % Allowed : 14.23 % Favored : 82.30 % 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: -0.52 (0.16), residues: 3048 helix: 0.92 (0.15), residues: 1210 sheet: -1.33 (0.25), residues: 408 loop : -1.13 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.006 0.001 HIS D 477 PHE 0.026 0.002 PHE C 183 TYR 0.014 0.001 TYR C 251 ARG 0.004 0.000 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 267 time to evaluate : 2.893 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: A 39 MET cc_start: 0.7036 (mmp) cc_final: 0.6417 (tmm) REVERT: A 162 MET cc_start: 0.8696 (mmt) cc_final: 0.8462 (mmt) REVERT: A 306 MET cc_start: 0.4675 (tmm) cc_final: 0.4052 (ttt) REVERT: A 331 MET cc_start: 0.5840 (tpp) cc_final: 0.5637 (tpp) REVERT: A 434 VAL cc_start: 0.6060 (m) cc_final: 0.5741 (m) REVERT: A 475 TYR cc_start: 0.7952 (p90) cc_final: 0.7749 (p90) REVERT: A 701 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7512 (tmm) REVERT: A 761 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8332 (m-10) REVERT: A 790 GLU cc_start: 0.7701 (pm20) cc_final: 0.7105 (pt0) REVERT: A 823 MET cc_start: 0.7701 (ptp) cc_final: 0.6879 (mmm) REVERT: B 153 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8124 (tp30) REVERT: B 354 MET cc_start: 0.7797 (tpp) cc_final: 0.7558 (tpp) REVERT: B 654 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 762 MET cc_start: 0.6569 (mtm) cc_final: 0.6348 (mtm) REVERT: C 114 ASP cc_start: 0.8158 (m-30) cc_final: 0.7622 (t0) REVERT: C 135 MET cc_start: 0.4709 (pmm) cc_final: 0.4289 (mtp) REVERT: C 576 PHE cc_start: 0.4343 (t80) cc_final: 0.3985 (t80) REVERT: C 606 TRP cc_start: 0.6906 (m100) cc_final: 0.6223 (m100) REVERT: C 609 TRP cc_start: 0.7571 (m100) cc_final: 0.7116 (m100) REVERT: C 790 GLU cc_start: 0.7553 (pm20) cc_final: 0.6773 (pt0) REVERT: C 823 MET cc_start: 0.5745 (ptp) cc_final: 0.5149 (mmm) REVERT: D 163 ILE cc_start: 0.8599 (tp) cc_final: 0.8313 (tt) REVERT: D 527 ILE cc_start: 0.8742 (mp) cc_final: 0.8505 (mp) REVERT: D 570 VAL cc_start: 0.6904 (OUTLIER) cc_final: 0.6668 (p) REVERT: D 571 HIS cc_start: 0.7212 (m90) cc_final: 0.6866 (t-90) REVERT: D 641 MET cc_start: 0.8696 (tpp) cc_final: 0.8492 (tpt) outliers start: 92 outliers final: 57 residues processed: 341 average time/residue: 0.3398 time to fit residues: 187.5832 Evaluate side-chains 303 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 242 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 761 TYR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 780 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 265 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN A 615 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25158 Z= 0.300 Angle : 0.608 8.864 34118 Z= 0.313 Chirality : 0.044 0.200 3886 Planarity : 0.004 0.071 4290 Dihedral : 4.562 42.689 3675 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.69 % Allowed : 14.87 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 3048 helix: 0.75 (0.15), residues: 1214 sheet: -1.64 (0.24), residues: 422 loop : -1.16 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 55 HIS 0.034 0.002 HIS B 780 PHE 0.025 0.002 PHE C 183 TYR 0.029 0.002 TYR A 251 ARG 0.007 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 251 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7189 (mmp) cc_final: 0.6519 (tmm) REVERT: A 162 MET cc_start: 0.8737 (mmt) cc_final: 0.8494 (mmt) REVERT: A 306 MET cc_start: 0.4692 (tmm) cc_final: 0.4037 (ttt) REVERT: A 434 VAL cc_start: 0.7679 (m) cc_final: 0.7271 (m) REVERT: A 475 TYR cc_start: 0.8112 (p90) cc_final: 0.7794 (p90) REVERT: A 476 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6596 (p0) REVERT: A 701 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7519 (tmm) REVERT: A 761 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8448 (m-10) REVERT: A 823 MET cc_start: 0.7759 (ptp) cc_final: 0.7005 (mmm) REVERT: B 74 MET cc_start: 0.4612 (ppp) cc_final: 0.4054 (ppp) REVERT: B 654 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 700 SER cc_start: 0.7238 (m) cc_final: 0.6696 (m) REVERT: B 818 MET cc_start: 0.5168 (ppp) cc_final: 0.4945 (ppp) REVERT: C 39 MET cc_start: 0.7653 (tmm) cc_final: 0.7236 (tmm) REVERT: C 114 ASP cc_start: 0.8271 (m-30) cc_final: 0.7829 (t0) REVERT: C 135 MET cc_start: 0.5229 (pmm) cc_final: 0.4782 (mmm) REVERT: C 162 MET cc_start: 0.8634 (mmt) cc_final: 0.8316 (mmt) REVERT: C 576 PHE cc_start: 0.4514 (t80) cc_final: 0.4147 (t80) REVERT: C 606 TRP cc_start: 0.6906 (m100) cc_final: 0.6301 (m100) REVERT: C 609 TRP cc_start: 0.7683 (m100) cc_final: 0.7449 (m100) REVERT: C 645 TYR cc_start: 0.7889 (t80) cc_final: 0.7592 (t80) REVERT: C 653 MET cc_start: 0.8640 (ttt) cc_final: 0.8275 (tpt) REVERT: C 823 MET cc_start: 0.5997 (ptp) cc_final: 0.5395 (mmm) REVERT: D 570 VAL cc_start: 0.6963 (OUTLIER) cc_final: 0.6728 (p) REVERT: D 571 HIS cc_start: 0.7334 (m90) cc_final: 0.7028 (t-90) REVERT: D 641 MET cc_start: 0.8696 (tpp) cc_final: 0.8477 (tpt) REVERT: D 780 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.7915 (m-70) outliers start: 98 outliers final: 69 residues processed: 326 average time/residue: 0.3317 time to fit residues: 177.4247 Evaluate side-chains 306 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 231 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 761 TYR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 640 ILE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 734 VAL Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 41 MET Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9980 chunk 266 optimal weight: 0.7980 chunk 58 optimal weight: 0.0050 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 782 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25158 Z= 0.151 Angle : 0.551 9.215 34118 Z= 0.276 Chirality : 0.042 0.167 3886 Planarity : 0.004 0.061 4290 Dihedral : 4.230 40.590 3675 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.97 % Allowed : 15.93 % Favored : 81.10 % 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: -0.64 (0.16), residues: 3048 helix: 0.75 (0.15), residues: 1218 sheet: -1.45 (0.26), residues: 372 loop : -1.12 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.007 0.001 HIS B 780 PHE 0.021 0.001 PHE C 183 TYR 0.011 0.001 TYR A 180 ARG 0.006 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 259 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6978 (mmp) cc_final: 0.6341 (tmm) REVERT: A 306 MET cc_start: 0.4670 (tmm) cc_final: 0.4022 (ttt) REVERT: A 434 VAL cc_start: 0.7511 (m) cc_final: 0.7100 (m) REVERT: A 761 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: A 790 GLU cc_start: 0.7585 (pm20) cc_final: 0.7196 (pt0) REVERT: A 823 MET cc_start: 0.7755 (ptp) cc_final: 0.7020 (mmm) REVERT: B 74 MET cc_start: 0.5050 (ppp) cc_final: 0.4544 (ppp) REVERT: B 153 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 546 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7510 (pt) REVERT: B 636 TRP cc_start: 0.5325 (t-100) cc_final: 0.5020 (t-100) REVERT: B 654 PHE cc_start: 0.8630 (m-80) cc_final: 0.8299 (t80) REVERT: C 39 MET cc_start: 0.7599 (tmm) cc_final: 0.7380 (tmm) REVERT: C 135 MET cc_start: 0.4999 (pmm) cc_final: 0.4459 (mtp) REVERT: C 162 MET cc_start: 0.8444 (mmt) cc_final: 0.8163 (mmt) REVERT: C 576 PHE cc_start: 0.4419 (t80) cc_final: 0.4056 (t80) REVERT: C 606 TRP cc_start: 0.6910 (m100) cc_final: 0.6346 (m100) REVERT: C 609 TRP cc_start: 0.7660 (m100) cc_final: 0.7131 (m100) REVERT: C 653 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8240 (tpt) REVERT: C 790 GLU cc_start: 0.7582 (pm20) cc_final: 0.7146 (pt0) REVERT: C 823 MET cc_start: 0.6120 (ptp) cc_final: 0.5623 (mmm) REVERT: D 570 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6770 (p) REVERT: D 571 HIS cc_start: 0.7346 (m90) cc_final: 0.7053 (t-90) REVERT: D 641 MET cc_start: 0.8672 (tpp) cc_final: 0.8454 (tpt) outliers start: 79 outliers final: 58 residues processed: 317 average time/residue: 0.3143 time to fit residues: 166.3299 Evaluate side-chains 304 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 242 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 761 TYR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 272 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 0.0170 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS D 782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25158 Z= 0.162 Angle : 0.556 10.887 34118 Z= 0.277 Chirality : 0.042 0.164 3886 Planarity : 0.004 0.053 4290 Dihedral : 4.127 39.289 3674 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.12 % Allowed : 16.57 % Favored : 80.31 % 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: -0.63 (0.16), residues: 3048 helix: 0.78 (0.15), residues: 1216 sheet: -1.49 (0.26), residues: 376 loop : -1.13 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.003 0.001 HIS D 477 PHE 0.035 0.001 PHE C 396 TYR 0.015 0.001 TYR C 645 ARG 0.004 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 251 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7072 (mmp) cc_final: 0.6405 (tmm) REVERT: A 306 MET cc_start: 0.4840 (tmm) cc_final: 0.4114 (ttt) REVERT: A 790 GLU cc_start: 0.7578 (pm20) cc_final: 0.7229 (pt0) REVERT: A 823 MET cc_start: 0.7758 (ptp) cc_final: 0.7021 (mmm) REVERT: B 74 MET cc_start: 0.5100 (ppp) cc_final: 0.4633 (ppp) REVERT: B 105 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8687 (p) REVERT: B 153 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 273 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7461 (t0) REVERT: B 470 MET cc_start: 0.8749 (ttp) cc_final: 0.8338 (ttm) REVERT: B 546 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7498 (pt) REVERT: B 636 TRP cc_start: 0.5365 (t-100) cc_final: 0.5097 (t-100) REVERT: B 654 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 818 MET cc_start: 0.5139 (ppp) cc_final: 0.4898 (ppp) REVERT: C 39 MET cc_start: 0.7599 (tmm) cc_final: 0.7295 (tmm) REVERT: C 135 MET cc_start: 0.4995 (pmm) cc_final: 0.4454 (mtp) REVERT: C 145 PHE cc_start: 0.7367 (m-80) cc_final: 0.6244 (m-80) REVERT: C 162 MET cc_start: 0.8475 (mmt) cc_final: 0.8117 (mmt) REVERT: C 576 PHE cc_start: 0.4481 (t80) cc_final: 0.4094 (t80) REVERT: C 606 TRP cc_start: 0.6853 (m100) cc_final: 0.6318 (m100) REVERT: C 609 TRP cc_start: 0.7660 (m100) cc_final: 0.7154 (m100) REVERT: C 653 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (tpt) REVERT: C 790 GLU cc_start: 0.7686 (pm20) cc_final: 0.7195 (pt0) REVERT: C 823 MET cc_start: 0.5919 (ptp) cc_final: 0.5404 (mmm) REVERT: D 41 MET cc_start: 0.7646 (ptm) cc_final: 0.6903 (ptt) REVERT: D 570 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6799 (p) REVERT: D 571 HIS cc_start: 0.7428 (m90) cc_final: 0.7080 (t-90) REVERT: D 641 MET cc_start: 0.8641 (tpp) cc_final: 0.8430 (tpt) REVERT: D 780 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.8122 (m-70) outliers start: 83 outliers final: 59 residues processed: 310 average time/residue: 0.3147 time to fit residues: 162.3177 Evaluate side-chains 306 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 272 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.9980 chunk 117 optimal weight: 0.0270 chunk 176 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 268 optimal weight: 0.0020 overall best weight: 0.5446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN D 375 ASN D 477 HIS D 782 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25158 Z= 0.148 Angle : 0.565 12.143 34118 Z= 0.279 Chirality : 0.042 0.190 3886 Planarity : 0.003 0.051 4290 Dihedral : 3.991 31.677 3673 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.09 % Allowed : 16.98 % Favored : 79.93 % 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: -0.59 (0.16), residues: 3048 helix: 0.83 (0.15), residues: 1210 sheet: -1.42 (0.26), residues: 372 loop : -1.12 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 284 HIS 0.009 0.001 HIS D 477 PHE 0.023 0.001 PHE C 183 TYR 0.012 0.001 TYR A 761 ARG 0.005 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 250 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.6989 (mmp) cc_final: 0.6252 (tmm) REVERT: A 306 MET cc_start: 0.5028 (tmm) cc_final: 0.4149 (ttt) REVERT: A 790 GLU cc_start: 0.7615 (pm20) cc_final: 0.7286 (pt0) REVERT: A 823 MET cc_start: 0.7727 (ptp) cc_final: 0.6997 (mmm) REVERT: B 74 MET cc_start: 0.4931 (ppp) cc_final: 0.4472 (ppp) REVERT: B 105 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 153 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 163 ILE cc_start: 0.8942 (tp) cc_final: 0.8723 (tt) REVERT: B 273 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7387 (t0) REVERT: B 470 MET cc_start: 0.8711 (ttp) cc_final: 0.8270 (ttm) REVERT: B 546 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7479 (pt) REVERT: B 636 TRP cc_start: 0.5371 (t-100) cc_final: 0.5116 (t-100) REVERT: B 654 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 39 MET cc_start: 0.7739 (tmm) cc_final: 0.7340 (tmm) REVERT: C 135 MET cc_start: 0.4907 (pmm) cc_final: 0.4376 (mtp) REVERT: C 145 PHE cc_start: 0.7131 (m-80) cc_final: 0.6579 (m-80) REVERT: C 162 MET cc_start: 0.8458 (mmt) cc_final: 0.8073 (mmt) REVERT: C 200 MET cc_start: 0.7820 (mmm) cc_final: 0.6778 (tpt) REVERT: C 576 PHE cc_start: 0.4464 (t80) cc_final: 0.4076 (t80) REVERT: C 606 TRP cc_start: 0.6927 (m100) cc_final: 0.6375 (m100) REVERT: C 609 TRP cc_start: 0.7653 (m100) cc_final: 0.7168 (m100) REVERT: C 653 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8295 (tpt) REVERT: C 701 MET cc_start: 0.7999 (tmm) cc_final: 0.7565 (tmm) REVERT: C 790 GLU cc_start: 0.7670 (pm20) cc_final: 0.7311 (pt0) REVERT: C 823 MET cc_start: 0.5951 (ptp) cc_final: 0.5474 (mmm) REVERT: D 570 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6793 (p) REVERT: D 571 HIS cc_start: 0.7522 (m90) cc_final: 0.7163 (t-90) REVERT: D 641 MET cc_start: 0.8633 (tpp) cc_final: 0.8396 (tpt) REVERT: D 780 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.8036 (m170) outliers start: 82 outliers final: 65 residues processed: 308 average time/residue: 0.3216 time to fit residues: 164.6010 Evaluate side-chains 313 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 241 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 523 ASP Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25158 Z= 0.299 Angle : 0.646 13.491 34118 Z= 0.324 Chirality : 0.044 0.183 3886 Planarity : 0.004 0.053 4290 Dihedral : 4.488 36.395 3673 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 3.01 % Allowed : 17.36 % Favored : 79.63 % 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 (0.16), residues: 3048 helix: 0.74 (0.15), residues: 1214 sheet: -1.69 (0.24), residues: 412 loop : -1.12 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 284 HIS 0.044 0.001 HIS D 477 PHE 0.029 0.002 PHE B 533 TYR 0.027 0.002 TYR C 475 ARG 0.005 0.001 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 239 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.7133 (mmp) cc_final: 0.6437 (tmm) REVERT: A 114 ASP cc_start: 0.8066 (m-30) cc_final: 0.7833 (t0) REVERT: A 306 MET cc_start: 0.4980 (tmm) cc_final: 0.4266 (ttt) REVERT: B 74 MET cc_start: 0.4973 (ppp) cc_final: 0.4551 (ppp) REVERT: B 105 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8876 (p) REVERT: B 188 GLU cc_start: 0.8432 (pm20) cc_final: 0.8150 (pm20) REVERT: B 470 MET cc_start: 0.8858 (ttp) cc_final: 0.8526 (ttm) REVERT: B 546 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7571 (pt) REVERT: B 636 TRP cc_start: 0.5568 (t-100) cc_final: 0.5221 (t-100) REVERT: B 654 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8335 (t80) REVERT: B 818 MET cc_start: 0.4904 (ppp) cc_final: 0.4623 (ppp) REVERT: C 39 MET cc_start: 0.7706 (tmm) cc_final: 0.7167 (tmm) REVERT: C 135 MET cc_start: 0.5520 (pmm) cc_final: 0.5024 (mtp) REVERT: C 145 PHE cc_start: 0.7401 (m-80) cc_final: 0.6898 (m-80) REVERT: C 162 MET cc_start: 0.8609 (mmt) cc_final: 0.8333 (mmt) REVERT: C 175 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8023 (p) REVERT: C 200 MET cc_start: 0.8124 (mmm) cc_final: 0.7184 (tpt) REVERT: C 272 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7756 (t80) REVERT: C 606 TRP cc_start: 0.6949 (m100) cc_final: 0.6408 (m100) REVERT: C 609 TRP cc_start: 0.7685 (m100) cc_final: 0.7289 (m100) REVERT: C 653 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8341 (tpt) REVERT: C 701 MET cc_start: 0.8269 (tmm) cc_final: 0.7745 (tmm) REVERT: C 790 GLU cc_start: 0.7687 (pm20) cc_final: 0.7394 (pt0) REVERT: C 823 MET cc_start: 0.5979 (ptp) cc_final: 0.5379 (mmm) REVERT: D 570 VAL cc_start: 0.7092 (OUTLIER) cc_final: 0.6819 (p) REVERT: D 571 HIS cc_start: 0.7485 (m90) cc_final: 0.7136 (t-90) REVERT: D 641 MET cc_start: 0.8612 (tpp) cc_final: 0.8389 (tpt) REVERT: D 702 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7493 (mmt) REVERT: D 780 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.7713 (m-70) outliers start: 80 outliers final: 58 residues processed: 299 average time/residue: 0.3387 time to fit residues: 167.8478 Evaluate side-chains 291 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 272 PHE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 655 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 6.9990 chunk 177 optimal weight: 0.0670 chunk 137 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 30.0000 chunk 280 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 192 optimal weight: 0.0570 overall best weight: 1.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS A 482 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25158 Z= 0.200 Angle : 0.610 14.583 34118 Z= 0.303 Chirality : 0.043 0.181 3886 Planarity : 0.004 0.057 4290 Dihedral : 4.404 34.600 3673 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.01 % Rotamer: Outliers : 2.75 % Allowed : 18.03 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.16), residues: 3048 helix: 0.77 (0.15), residues: 1212 sheet: -1.60 (0.25), residues: 376 loop : -1.16 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 284 HIS 0.006 0.001 HIS A 405 PHE 0.026 0.001 PHE C 396 TYR 0.033 0.001 TYR C 475 ARG 0.009 0.000 ARG D 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 235 time to evaluate : 2.786 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 39 MET cc_start: 0.7009 (mmp) cc_final: 0.6277 (tmm) REVERT: A 114 ASP cc_start: 0.8023 (m-30) cc_final: 0.7757 (m-30) REVERT: A 306 MET cc_start: 0.5028 (tmm) cc_final: 0.4263 (ttt) REVERT: A 823 MET cc_start: 0.7613 (ptp) cc_final: 0.6867 (mmm) REVERT: B 74 MET cc_start: 0.4999 (ppp) cc_final: 0.4545 (ppp) REVERT: B 105 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8805 (p) REVERT: B 470 MET cc_start: 0.8793 (ttp) cc_final: 0.8407 (ttm) REVERT: B 546 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7590 (pt) REVERT: B 636 TRP cc_start: 0.5571 (t-100) cc_final: 0.5256 (t-100) REVERT: B 654 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8301 (t80) REVERT: C 39 MET cc_start: 0.7551 (tmm) cc_final: 0.7155 (tmm) REVERT: C 135 MET cc_start: 0.5432 (pmm) cc_final: 0.4940 (mtp) REVERT: C 145 PHE cc_start: 0.7196 (m-80) cc_final: 0.6644 (m-80) REVERT: C 162 MET cc_start: 0.8601 (mmt) cc_final: 0.8321 (mmt) REVERT: C 175 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (p) REVERT: C 200 MET cc_start: 0.7893 (mmm) cc_final: 0.7032 (tpt) REVERT: C 606 TRP cc_start: 0.6869 (m100) cc_final: 0.6296 (m100) REVERT: C 609 TRP cc_start: 0.7827 (m100) cc_final: 0.7425 (m100) REVERT: C 645 TYR cc_start: 0.7678 (t80) cc_final: 0.7451 (t80) REVERT: C 653 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8255 (tpt) REVERT: C 790 GLU cc_start: 0.7727 (pm20) cc_final: 0.7452 (pt0) REVERT: C 823 MET cc_start: 0.6026 (ptp) cc_final: 0.5625 (mmm) REVERT: D 570 VAL cc_start: 0.7103 (OUTLIER) cc_final: 0.6828 (p) REVERT: D 571 HIS cc_start: 0.7480 (m90) cc_final: 0.7134 (t-90) REVERT: D 780 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8035 (m-70) outliers start: 73 outliers final: 56 residues processed: 287 average time/residue: 0.3282 time to fit residues: 156.1660 Evaluate side-chains 289 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 226 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 177 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain A residue 726 ASP Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 817 MET Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 780 HIS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 677 SER Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 758 THR Chi-restraints excluded: chain C residue 817 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 518 THR Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 780 HIS Chi-restraints excluded: chain D residue 795 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 482 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.119253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.090450 restraints weight = 79220.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.093164 restraints weight = 43914.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.094933 restraints weight = 30223.192| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25158 Z= 0.200 Angle : 0.608 13.752 34118 Z= 0.301 Chirality : 0.043 0.176 3886 Planarity : 0.004 0.059 4290 Dihedral : 4.384 32.862 3673 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 3.01 % Allowed : 18.15 % Favored : 78.84 % 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 (0.16), residues: 3048 helix: 0.73 (0.15), residues: 1220 sheet: -1.60 (0.25), residues: 376 loop : -1.16 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.006 0.001 HIS D 477 PHE 0.032 0.001 PHE D 42 TYR 0.022 0.001 TYR C 475 ARG 0.003 0.000 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.10 seconds wall clock time: 91 minutes 10.43 seconds (5470.43 seconds total)