Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 03:57:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2023/7eot_31230_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2023/7eot_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_2023/7eot_31230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2023/7eot_31230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2023/7eot_31230_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eot_31230/04_2023/7eot_31230_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 chiralities: 7 Time building chain proxies: 12.79, 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: 9.92 Conformation dependent library (CDL) restraints added in 3.4 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: 3.13 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: 7.33 Time building geometry restraints manager: 10.65 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: 13628 11.99 - 23.97: 800 23.97 - 35.96: 287 35.96 - 47.94: 83 47.94 - 59.93: 14 Dihedral angle restraints: 14812 sinusoidal: 5864 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 14809 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.940 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 58.710 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.290 ------------------------------------------------------------------------------- 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 : 9.234 59.930 8978 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 % 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 *********************** 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 : 2.641 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 outliers start: 59 outliers final: 13 residues processed: 640 average time/residue: 0.3969 time to fit residues: 382.4157 Evaluate side-chains 337 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 324 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2257 time to fit residues: 9.4466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 8.9990 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 145 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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 48 GLN ** B 67 HIS ** 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 B 780 HIS C 193 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 HIS D 477 HIS ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 25158 Z= 0.345 Angle : 0.682 9.933 34118 Z= 0.350 Chirality : 0.046 0.243 3886 Planarity : 0.005 0.076 4290 Dihedral : 4.147 63.060 3302 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 3.54 % 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: -0.51 (0.16), residues: 3048 helix: 1.03 (0.15), residues: 1212 sheet: -1.30 (0.27), residues: 370 loop : -1.24 (0.16), residues: 1466 *********************** 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 418 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 324 time to evaluate : 2.979 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 outliers start: 94 outliers final: 51 residues processed: 395 average time/residue: 0.3609 time to fit residues: 223.6493 Evaluate side-chains 297 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 246 time to evaluate : 2.645 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2200 time to fit residues: 24.5140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 0.1980 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 223 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 111 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 85 HIS ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 25158 Z= 0.160 Angle : 0.555 8.479 34118 Z= 0.280 Chirality : 0.042 0.165 3886 Planarity : 0.004 0.058 4290 Dihedral : 3.882 54.849 3302 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.84 % 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: -0.57 (0.15), residues: 3048 helix: 0.89 (0.15), residues: 1208 sheet: -1.22 (0.26), residues: 404 loop : -1.19 (0.17), residues: 1436 *********************** 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 331 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 2.992 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 outliers start: 49 outliers final: 14 residues processed: 323 average time/residue: 0.3322 time to fit residues: 176.3958 Evaluate side-chains 259 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2232 time to fit residues: 9.6769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 264 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 A 697 ASN 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 25158 Z= 0.251 Angle : 0.570 7.682 34118 Z= 0.293 Chirality : 0.043 0.223 3886 Planarity : 0.004 0.053 4290 Dihedral : 4.051 52.470 3302 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3048 helix: 0.79 (0.15), residues: 1208 sheet: -1.48 (0.25), residues: 410 loop : -1.16 (0.17), residues: 1430 *********************** 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 318 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 255 time to evaluate : 2.962 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 outliers start: 63 outliers final: 25 residues processed: 297 average time/residue: 0.3407 time to fit residues: 164.9176 Evaluate side-chains 255 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 2.817 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.2226 time to fit residues: 14.2067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 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 193 ASN ** C 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 196 GLN ** 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 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 25158 Z= 0.334 Angle : 0.655 9.673 34118 Z= 0.338 Chirality : 0.045 0.187 3886 Planarity : 0.004 0.057 4290 Dihedral : 4.614 45.167 3302 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 2.03 % 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: -0.94 (0.15), residues: 3048 helix: 0.59 (0.15), residues: 1216 sheet: -1.98 (0.24), residues: 382 loop : -1.25 (0.17), residues: 1450 *********************** 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 294 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 240 time to evaluate : 2.813 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 outliers start: 54 outliers final: 23 residues processed: 283 average time/residue: 0.3391 time to fit residues: 156.5017 Evaluate side-chains 235 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 2.770 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.2323 time to fit residues: 13.8258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 296 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 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 D 40 GLN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 GLN ** 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 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5148 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= 0.188 Angle : 0.575 9.045 34118 Z= 0.291 Chirality : 0.043 0.203 3886 Planarity : 0.004 0.076 4290 Dihedral : 4.276 38.047 3302 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 1.47 % 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: -0.82 (0.15), residues: 3048 helix: 0.70 (0.15), residues: 1216 sheet: -1.71 (0.25), residues: 364 loop : -1.27 (0.17), residues: 1468 *********************** 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 290 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 282 average time/residue: 0.3388 time to fit residues: 157.2713 Evaluate side-chains 242 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2262 time to fit residues: 11.0511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 0.0570 chunk 216 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 136 optimal weight: 0.0060 overall best weight: 1.4120 ------------------------------------------------------------------------------- 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 40 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 196 GLN ** 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 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 25158 Z= 0.203 Angle : 0.586 11.259 34118 Z= 0.294 Chirality : 0.043 0.176 3886 Planarity : 0.004 0.050 4290 Dihedral : 4.236 34.968 3302 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.02 % 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: -0.81 (0.15), residues: 3048 helix: 0.70 (0.15), residues: 1216 sheet: -1.77 (0.24), residues: 408 loop : -1.20 (0.17), residues: 1424 *********************** 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 262 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 253 average time/residue: 0.3412 time to fit residues: 142.0953 Evaluate side-chains 238 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2264 time to fit residues: 9.4719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.6980 chunk 117 optimal weight: 0.0070 chunk 176 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 0.1980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 482 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 ASN C 693 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 25158 Z= 0.159 Angle : 0.588 12.254 34118 Z= 0.291 Chirality : 0.043 0.240 3886 Planarity : 0.004 0.052 4290 Dihedral : 4.111 31.036 3302 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.83 % 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: -0.75 (0.15), residues: 3048 helix: 0.68 (0.15), residues: 1214 sheet: -1.57 (0.26), residues: 360 loop : -1.19 (0.17), residues: 1474 *********************** 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 257 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 235 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 249 average time/residue: 0.3609 time to fit residues: 148.7509 Evaluate side-chains 228 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 3.000 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2403 time to fit residues: 7.3180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 482 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25158 Z= 0.190 Angle : 0.585 10.929 34118 Z= 0.290 Chirality : 0.043 0.224 3886 Planarity : 0.004 0.053 4290 Dihedral : 4.160 31.327 3302 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer Outliers : 0.72 % 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: -0.74 (0.16), residues: 3048 helix: 0.72 (0.15), residues: 1214 sheet: -1.69 (0.24), residues: 404 loop : -1.14 (0.17), residues: 1430 *********************** 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 244 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 238 average time/residue: 0.3366 time to fit residues: 132.8881 Evaluate side-chains 227 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 2.745 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2343 time to fit residues: 8.2258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 304 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 0.0870 chunk 192 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN D 375 ASN D 477 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 25158 Z= 0.159 Angle : 0.597 12.668 34118 Z= 0.292 Chirality : 0.043 0.255 3886 Planarity : 0.004 0.055 4290 Dihedral : 4.095 30.648 3302 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.30 % 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: -0.69 (0.16), residues: 3048 helix: 0.73 (0.15), residues: 1206 sheet: -1.51 (0.26), residues: 364 loop : -1.16 (0.17), residues: 1478 ********************** 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 231 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 223 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 227 average time/residue: 0.3367 time to fit residues: 126.5006 Evaluate side-chains 222 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 218 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2651 time to fit residues: 5.7352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 223 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 243 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 40 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 705 HIS ** 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 ** D 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.118537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.090633 restraints weight = 79119.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.093082 restraints weight = 46912.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.093942 restraints weight = 33448.204| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25158 Z= 0.213 Angle : 0.608 11.805 34118 Z= 0.300 Chirality : 0.044 0.273 3886 Planarity : 0.004 0.056 4290 Dihedral : 4.226 32.171 3302 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.61 % Favored : 94.36 % Rotamer Outliers : 0.45 % 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: -0.76 (0.16), residues: 3048 helix: 0.71 (0.15), residues: 1222 sheet: -1.70 (0.24), residues: 410 loop : -1.17 (0.17), residues: 1416 =============================================================================== Job complete usr+sys time: 4304.66 seconds wall clock time: 80 minutes 22.01 seconds (4822.01 seconds total)