Starting phenix.real_space_refine on Thu Mar 5 18:02:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzl_48760/03_2026/9mzl_48760.cif" } resolution = 4.02 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 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= 0.003 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 15149 2.51 5 N 3896 2.21 5 O 4411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23592 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5906 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 28, 'TRANS': 717} Chain breaks: 3 Chain: "B" Number of atoms: 5806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5806 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 707} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5844 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 712} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5871 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 Time building chain proxies: 5.61, per 1000 atoms: 0.24 Number of scatterers: 23592 At special positions: 0 Unit cell: (108.12, 159, 180.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4411 8.00 N 3896 7.00 C 15149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A1001 " - " ASN A 430 " " NAG A1002 " - " ASN A 751 " " NAG A1003 " - " ASN A 423 " " NAG A1004 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 275 " " NAG C1002 " - " ASN C 412 " " NAG D1001 " - " ASN D 412 " " NAG E 1 " - " ASN A 275 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 974.0 milliseconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 32 sheets defined 45.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.884A pdb=" N ASN A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.252A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.504A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.633A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 298 removed outlier: 3.674A pdb=" N MET A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.614A pdb=" N GLN A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 366 removed outlier: 3.863A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.731A pdb=" N GLY A 419 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.717A pdb=" N ASP A 507 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.689A pdb=" N GLU A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 525' Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 567 through 581 removed outlier: 3.523A pdb=" N LEU A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 664 removed outlier: 3.687A pdb=" N GLY A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.829A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 4.305A pdb=" N MET A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 706 " --> pdb=" O TYR A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 3.758A pdb=" N LEU A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.547A pdb=" N VAL A 728 " --> pdb=" O GLY A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.530A pdb=" N ILE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 743 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 removed outlier: 3.945A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 821 through 835 removed outlier: 3.593A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.951A pdb=" N ALA B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.782A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.439A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.723A pdb=" N LEU B 182 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE B 183 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.148A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.671A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.954A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.574A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.571A pdb=" N ARG B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 4.123A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.818A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.839A pdb=" N LEU B 556 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 Processing helix chain 'B' and resid 633 through 661 removed outlier: 3.503A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 676 Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 699 through 710 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.674A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.799A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 798 removed outlier: 3.618A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 839 removed outlier: 4.006A pdb=" N ALA B 828 " --> pdb=" O PHE B 824 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.568A pdb=" N ALA C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 185 removed outlier: 3.989A pdb=" N LEU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.711A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 185 through 190' Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.221A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 260 through 264 removed outlier: 3.646A pdb=" N LEU C 264 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.210A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.597A pdb=" N VAL C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.512A pdb=" N ASP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 581 removed outlier: 3.656A pdb=" N MET C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 665 removed outlier: 3.689A pdb=" N ILE C 647 " --> pdb=" O PHE C 643 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU C 662 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 removed outlier: 3.832A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 670 through 675' Processing helix chain 'C' and resid 676 through 680 removed outlier: 4.403A pdb=" N LYS C 679 " --> pdb=" O CYS C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 4.192A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS C 695 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.980A pdb=" N LYS C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 707 " --> pdb=" O ASP C 703 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 708 " --> pdb=" O LYS C 704 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 791 through 799 removed outlier: 3.988A pdb=" N LYS C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 816 removed outlier: 3.517A pdb=" N LEU C 815 " --> pdb=" O ALA C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 836 removed outlier: 4.377A pdb=" N ILE C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.782A pdb=" N ALA D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 152 through 168 removed outlier: 3.502A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.013A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 Processing helix chain 'D' and resid 286 through 300 Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.632A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.545A pdb=" N THR D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 4.077A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 3.719A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 555 removed outlier: 4.384A pdb=" N PHE D 555 " --> pdb=" O VAL D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 582 removed outlier: 3.588A pdb=" N TRP D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 657 Processing helix chain 'D' and resid 672 through 677 removed outlier: 3.611A pdb=" N CYS D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.621A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 711 removed outlier: 3.565A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.560A pdb=" N GLY D 724 " --> pdb=" O SER D 720 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 772 through 789 removed outlier: 3.901A pdb=" N ASP D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 799 removed outlier: 3.581A pdb=" N TRP D 799 " --> pdb=" O LYS D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 838 removed outlier: 3.744A pdb=" N ALA D 838 " --> pdb=" O SER D 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.510A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 147 " --> pdb=" O HIS A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.121A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 203 removed outlier: 7.099A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 280 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 437 Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.815A pdb=" N THR A 768 " --> pdb=" O ASP A 528 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA9, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 682 through 683 Processing sheet with id=AB2, first strand: chain 'B' and resid 34 through 43 removed outlier: 6.663A pdb=" N HIS B 34 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR B 77 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.138A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 202 through 203 removed outlier: 5.903A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 279 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 435 through 436 removed outlier: 7.223A pdb=" N VAL B 435 " --> pdb=" O ARG B 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.637A pdb=" N MET B 737 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 75 through 83 removed outlier: 6.158A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C 105 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE C 107 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 41 " --> pdb=" O PHE C 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 199 through 201 removed outlier: 6.390A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP C 229 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 175 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 280 removed outlier: 3.671A pdb=" N GLU C 400 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 368 through 370 removed outlier: 3.859A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 404 through 405 Processing sheet with id=AC5, first strand: chain 'C' and resid 432 through 433 Processing sheet with id=AC6, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC7, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 683 removed outlier: 6.899A pdb=" N GLU C 681 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU C 736 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY C 683 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLU C 738 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N TYR C 733 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ARG C 543 " --> pdb=" O TYR C 733 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 74 through 83 removed outlier: 5.788A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR D 77 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASP D 79 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLN D 81 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY D 40 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE D 83 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.751A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D 403 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.936A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 433 through 436 Processing sheet with id=AD4, first strand: chain 'D' and resid 513 through 517 removed outlier: 7.395A pdb=" N ALA D 515 " --> pdb=" O GLY D 767 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLY D 767 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.158A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2673 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: 4.55 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7449 1.34 - 1.46: 5540 1.46 - 1.58: 10882 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 24103 Sorted by residual: bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.73e+00 bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.32e-02 5.74e+03 3.72e+00 bond pdb=" N THR B 652 " pdb=" CA THR B 652 " ideal model delta sigma weight residual 1.459 1.482 -0.022 1.18e-02 7.18e+03 3.55e+00 bond pdb=" N THR C 652 " pdb=" CA THR C 652 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.34e+00 bond pdb=" CB LYS C 704 " pdb=" CG LYS C 704 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.13e+00 ... (remaining 24098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 32262 2.33 - 4.65: 294 4.65 - 6.98: 55 6.98 - 9.30: 18 9.30 - 11.63: 5 Bond angle restraints: 32634 Sorted by residual: angle pdb=" N ILE B 823 " pdb=" CA ILE B 823 " pdb=" C ILE B 823 " ideal model delta sigma weight residual 111.91 107.68 4.23 8.90e-01 1.26e+00 2.26e+01 angle pdb=" N ILE A 759 " pdb=" CA ILE A 759 " pdb=" C ILE A 759 " ideal model delta sigma weight residual 113.71 109.51 4.20 9.50e-01 1.11e+00 1.95e+01 angle pdb=" CA LYS C 704 " pdb=" CB LYS C 704 " pdb=" CG LYS C 704 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CB MET B 50 " pdb=" CG MET B 50 " pdb=" SD MET B 50 " ideal model delta sigma weight residual 112.70 124.33 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N MET A 664 " pdb=" CA MET A 664 " pdb=" C MET A 664 " ideal model delta sigma weight residual 113.16 108.47 4.69 1.24e+00 6.50e-01 1.43e+01 ... (remaining 32629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12393 17.85 - 35.69: 1619 35.69 - 53.54: 432 53.54 - 71.39: 62 71.39 - 89.24: 17 Dihedral angle restraints: 14523 sinusoidal: 5945 harmonic: 8578 Sorted by residual: dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual -86.00 -17.59 -68.41 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual 93.00 151.81 -58.81 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA PRO C 442 " pdb=" C PRO C 442 " pdb=" N TYR C 443 " pdb=" CA TYR C 443 " ideal model delta harmonic sigma weight residual -180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 14520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3399 0.071 - 0.142: 310 0.142 - 0.214: 8 0.214 - 0.285: 1 0.285 - 0.356: 2 Chirality restraints: 3720 Sorted by residual: chirality pdb=" C1 NAG A1002 " pdb=" ND2 ASN A 751 " pdb=" C2 NAG A1002 " pdb=" O5 NAG A1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 412 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB THR D 257 " pdb=" CA THR D 257 " pdb=" OG1 THR D 257 " pdb=" CG2 THR D 257 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 3717 not shown) Planarity restraints: 4106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 304 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO B 305 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 663 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C ARG A 663 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 663 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 664 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 140 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" CG ASP B 140 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 140 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 140 " 0.012 2.00e-02 2.50e+03 ... (remaining 4103 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 10616 2.94 - 3.43: 26093 3.43 - 3.92: 39948 3.92 - 4.41: 45351 4.41 - 4.90: 70033 Nonbonded interactions: 192041 Sorted by model distance: nonbonded pdb=" O ASP B 140 " pdb=" OD1 ASP B 140 " model vdw 2.453 3.040 nonbonded pdb=" O ILE C 648 " pdb=" OG1 THR C 652 " model vdw 2.541 3.040 nonbonded pdb=" N ASP C 776 " pdb=" OD1 ASP C 776 " model vdw 2.546 3.120 nonbonded pdb=" O ASP B 87 " pdb=" OD1 ASP B 87 " model vdw 2.558 3.040 nonbonded pdb=" N ASN A 116 " pdb=" OD1 ASN A 116 " model vdw 2.566 3.120 ... (remaining 192036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 415 or resid 432 through 447 or resid 452 throu \ gh 544 or resid 546 through 582 or resid 632 through 633 or (resid 634 and (name \ N or name CA or name C or name O or name CB )) or resid 635 through 661 or (res \ id 662 and (name N or name CA or name C or name O or name CB )) or resid 663 thr \ ough 805 or resid 816 through 835 or resid 1004)) selection = (chain 'B' and (resid 33 through 415 or resid 432 through 447 or resid 452 throu \ gh 544 or resid 546 or resid 550 through 582 or resid 632 through 835 or resid 1 \ 002)) selection = (chain 'C' and (resid 33 through 415 or resid 432 through 544 or resid 549 throu \ gh 630 or resid 632 through 805 or resid 816 through 835 or resid 1002)) selection = (chain 'D' and (resid 33 through 415 or resid 432 through 447 or resid 452 throu \ gh 544 or resid 546 or resid 550 through 633 or (resid 634 and (name N or name C \ A or name C or name O or name CB )) or resid 635 through 661 or (resid 662 and ( \ name N or name CA or name C or name O or name CB )) or resid 663 through 805 or \ resid 816 through 835 or resid 1001)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.200 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.002 0.053 24123 Z= 0.108 Angle : 0.606 11.630 32686 Z= 0.296 Chirality : 0.041 0.356 3720 Planarity : 0.003 0.066 4096 Dihedral : 16.791 89.235 8979 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.99 % Allowed : 26.28 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 2929 helix: -0.18 (0.14), residues: 1183 sheet: -1.40 (0.29), residues: 349 loop : -1.53 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 523 TYR 0.020 0.001 TYR B 488 PHE 0.021 0.001 PHE B 642 TRP 0.015 0.001 TRP B 296 HIS 0.004 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00223 (24103) covalent geometry : angle 0.59936 (32634) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.59310 ( 16) hydrogen bonds : bond 0.23444 ( 924) hydrogen bonds : angle 7.70631 ( 2673) link_BETA1-4 : bond 0.00241 ( 2) link_BETA1-4 : angle 1.44067 ( 6) link_NAG-ASN : bond 0.00714 ( 10) link_NAG-ASN : angle 3.04317 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.9307 (p) cc_final: 0.9006 (p) REVERT: A 323 MET cc_start: 0.9194 (tpp) cc_final: 0.8465 (tpp) REVERT: A 340 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6107 (ppp) REVERT: A 576 CYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7973 (m) REVERT: A 691 MET cc_start: 0.9084 (ptp) cc_final: 0.8480 (pmm) REVERT: A 709 MET cc_start: 0.8722 (mpp) cc_final: 0.8089 (mtp) REVERT: A 764 TYR cc_start: 0.5900 (m-80) cc_final: 0.5382 (m-80) REVERT: A 770 MET cc_start: 0.8240 (tpp) cc_final: 0.7494 (mmm) REVERT: B 50 MET cc_start: 0.8666 (tpp) cc_final: 0.8146 (tpp) REVERT: B 210 ASP cc_start: 0.7705 (t0) cc_final: 0.7494 (t0) REVERT: B 218 MET cc_start: 0.8996 (tpp) cc_final: 0.8672 (mmm) REVERT: B 247 MET cc_start: 0.8074 (tpp) cc_final: 0.7508 (tpp) REVERT: B 298 MET cc_start: 0.8579 (mtm) cc_final: 0.8302 (mpp) REVERT: B 360 MET cc_start: 0.8346 (tpp) cc_final: 0.8007 (mmm) REVERT: B 533 PHE cc_start: 0.4010 (OUTLIER) cc_final: 0.3649 (p90) REVERT: B 534 MET cc_start: 0.3617 (pmm) cc_final: 0.3329 (pmm) REVERT: B 556 LEU cc_start: 0.8749 (mp) cc_final: 0.8491 (mp) REVERT: B 719 LYS cc_start: 0.8436 (pptt) cc_final: 0.8008 (ptpp) REVERT: B 737 MET cc_start: 0.4714 (mmp) cc_final: 0.4324 (mmm) REVERT: B 770 MET cc_start: 0.6263 (mmt) cc_final: 0.5099 (tpt) REVERT: C 140 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8744 (p0) REVERT: C 300 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8107 (tpt90) REVERT: C 402 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9242 (pt) REVERT: C 555 PHE cc_start: 0.7504 (m-80) cc_final: 0.7116 (m-80) REVERT: C 565 MET cc_start: 0.8562 (mmt) cc_final: 0.8267 (ppp) REVERT: C 566 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8510 (t80) REVERT: C 709 MET cc_start: 0.7543 (mpp) cc_final: 0.6955 (mpp) REVERT: C 737 MET cc_start: 0.7082 (ppp) cc_final: 0.6792 (ppp) REVERT: C 770 MET cc_start: 0.8401 (mmm) cc_final: 0.8160 (mmm) REVERT: D 197 LEU cc_start: 0.8991 (mt) cc_final: 0.8765 (mt) REVERT: D 229 ASP cc_start: 0.7571 (t70) cc_final: 0.7212 (t70) REVERT: D 247 MET cc_start: 0.8488 (tpp) cc_final: 0.8129 (tpp) REVERT: D 276 MET cc_start: 0.8760 (ppp) cc_final: 0.8172 (ppp) REVERT: D 340 MET cc_start: 0.8920 (mmm) cc_final: 0.8008 (mmm) REVERT: D 576 CYS cc_start: 0.8485 (t) cc_final: 0.8145 (m) REVERT: D 796 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8352 (mt-10) outliers start: 51 outliers final: 39 residues processed: 271 average time/residue: 0.1417 time to fit residues: 64.1833 Evaluate side-chains 271 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0270 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.0070 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 2.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN B 350 HIS ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 186 GLN C 232 HIS C 350 HIS ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.094444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070490 restraints weight = 97097.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.069943 restraints weight = 52768.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.070363 restraints weight = 41456.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070733 restraints weight = 38629.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.071104 restraints weight = 32225.144| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24123 Z= 0.179 Angle : 0.651 9.719 32686 Z= 0.330 Chirality : 0.043 0.327 3720 Planarity : 0.004 0.051 4096 Dihedral : 4.986 53.590 3440 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.12 % Allowed : 3.94 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 2929 helix: 0.40 (0.15), residues: 1224 sheet: -1.50 (0.28), residues: 356 loop : -1.45 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 384 TYR 0.031 0.002 TYR A 176 PHE 0.023 0.002 PHE D 533 TRP 0.021 0.001 TRP B 706 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00393 (24103) covalent geometry : angle 0.64272 (32634) SS BOND : bond 0.00235 ( 8) SS BOND : angle 0.86020 ( 16) hydrogen bonds : bond 0.04860 ( 924) hydrogen bonds : angle 5.38853 ( 2673) link_BETA1-4 : bond 0.00290 ( 2) link_BETA1-4 : angle 1.32970 ( 6) link_NAG-ASN : bond 0.00715 ( 10) link_NAG-ASN : angle 3.49046 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8937 (tpp) cc_final: 0.8436 (tpp) REVERT: A 340 MET cc_start: 0.6965 (ppp) cc_final: 0.5991 (ppp) REVERT: A 770 MET cc_start: 0.8255 (tpp) cc_final: 0.7576 (mmm) REVERT: B 218 MET cc_start: 0.9128 (tpp) cc_final: 0.8872 (tpp) REVERT: B 360 MET cc_start: 0.8298 (tpp) cc_final: 0.7968 (mmm) REVERT: B 406 ASP cc_start: 0.7605 (t70) cc_final: 0.7395 (m-30) REVERT: B 706 TRP cc_start: 0.8334 (t-100) cc_final: 0.7914 (t-100) REVERT: B 770 MET cc_start: 0.6061 (mmt) cc_final: 0.4914 (tpt) REVERT: C 534 MET cc_start: 0.7988 (ppp) cc_final: 0.7212 (ppp) REVERT: C 555 PHE cc_start: 0.7633 (m-80) cc_final: 0.7276 (m-80) REVERT: C 565 MET cc_start: 0.8624 (mmt) cc_final: 0.8187 (ptt) REVERT: D 197 LEU cc_start: 0.9012 (mt) cc_final: 0.8726 (mt) REVERT: D 229 ASP cc_start: 0.7584 (t70) cc_final: 0.7035 (t0) REVERT: D 247 MET cc_start: 0.8509 (tpp) cc_final: 0.8281 (tpp) REVERT: D 276 MET cc_start: 0.8910 (ppp) cc_final: 0.8297 (ppp) REVERT: D 340 MET cc_start: 0.8841 (tpt) cc_final: 0.8390 (tpt) REVERT: D 565 MET cc_start: 0.9095 (mpp) cc_final: 0.8730 (mmt) REVERT: D 572 LEU cc_start: 0.9287 (tp) cc_final: 0.8899 (tp) REVERT: D 576 CYS cc_start: 0.8512 (t) cc_final: 0.8239 (m) REVERT: D 796 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8435 (mt-10) outliers start: 3 outliers final: 0 residues processed: 299 average time/residue: 0.1438 time to fit residues: 71.1942 Evaluate side-chains 210 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 92 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065940 restraints weight = 97859.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068951 restraints weight = 55083.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069137 restraints weight = 32130.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069548 restraints weight = 26975.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.069623 restraints weight = 26120.668| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24123 Z= 0.170 Angle : 0.609 9.569 32686 Z= 0.307 Chirality : 0.042 0.339 3720 Planarity : 0.004 0.039 4096 Dihedral : 5.062 54.007 3440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.12 % Allowed : 4.64 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2929 helix: 0.51 (0.15), residues: 1230 sheet: -1.66 (0.28), residues: 342 loop : -1.47 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 543 TYR 0.019 0.001 TYR B 252 PHE 0.041 0.002 PHE C 153 TRP 0.021 0.001 TRP D 134 HIS 0.008 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00377 (24103) covalent geometry : angle 0.60058 (32634) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.69136 ( 16) hydrogen bonds : bond 0.03996 ( 924) hydrogen bonds : angle 5.05435 ( 2673) link_BETA1-4 : bond 0.00060 ( 2) link_BETA1-4 : angle 1.29688 ( 6) link_NAG-ASN : bond 0.00657 ( 10) link_NAG-ASN : angle 3.38664 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.9672 (mm) cc_final: 0.9470 (mm) REVERT: A 323 MET cc_start: 0.8861 (tpp) cc_final: 0.8516 (tpp) REVERT: A 340 MET cc_start: 0.6636 (ppp) cc_final: 0.6041 (ppp) REVERT: A 576 CYS cc_start: 0.8278 (m) cc_final: 0.8074 (m) REVERT: A 770 MET cc_start: 0.8242 (tpp) cc_final: 0.7557 (mmm) REVERT: B 218 MET cc_start: 0.9121 (tpp) cc_final: 0.8898 (tpp) REVERT: B 252 TYR cc_start: 0.8935 (m-80) cc_final: 0.8712 (m-10) REVERT: B 770 MET cc_start: 0.5949 (mmt) cc_final: 0.4881 (tpt) REVERT: C 555 PHE cc_start: 0.7624 (m-80) cc_final: 0.7249 (m-80) REVERT: C 565 MET cc_start: 0.8547 (mmt) cc_final: 0.8096 (ptt) REVERT: C 770 MET cc_start: 0.8397 (mmm) cc_final: 0.8142 (mmm) REVERT: D 89 PHE cc_start: 0.8935 (t80) cc_final: 0.8591 (t80) REVERT: D 229 ASP cc_start: 0.7491 (t70) cc_final: 0.7001 (t0) REVERT: D 247 MET cc_start: 0.8532 (tpp) cc_final: 0.8314 (tpp) REVERT: D 276 MET cc_start: 0.8772 (ppp) cc_final: 0.8422 (ppp) REVERT: D 298 MET cc_start: 0.9002 (tpp) cc_final: 0.8731 (tmm) REVERT: D 340 MET cc_start: 0.8777 (tpt) cc_final: 0.8394 (tpt) REVERT: D 565 MET cc_start: 0.9111 (mpp) cc_final: 0.8715 (mmt) REVERT: D 572 LEU cc_start: 0.9303 (tp) cc_final: 0.8894 (tp) REVERT: D 576 CYS cc_start: 0.8440 (t) cc_final: 0.8149 (m) REVERT: D 796 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8486 (mt-10) outliers start: 3 outliers final: 1 residues processed: 266 average time/residue: 0.1374 time to fit residues: 61.9948 Evaluate side-chains 207 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 241 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.092465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.067442 restraints weight = 97209.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067151 restraints weight = 57038.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067565 restraints weight = 46252.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068330 restraints weight = 39187.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068459 restraints weight = 33600.480| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24123 Z= 0.212 Angle : 0.641 12.441 32686 Z= 0.323 Chirality : 0.043 0.340 3720 Planarity : 0.004 0.047 4096 Dihedral : 5.282 53.895 3440 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 2929 helix: 0.47 (0.15), residues: 1237 sheet: -1.73 (0.27), residues: 349 loop : -1.55 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 431 TYR 0.024 0.002 TYR B 269 PHE 0.036 0.002 PHE D 735 TRP 0.025 0.001 TRP D 134 HIS 0.006 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00464 (24103) covalent geometry : angle 0.63156 (32634) SS BOND : bond 0.00389 ( 8) SS BOND : angle 0.98679 ( 16) hydrogen bonds : bond 0.03728 ( 924) hydrogen bonds : angle 5.00472 ( 2673) link_BETA1-4 : bond 0.00148 ( 2) link_BETA1-4 : angle 1.34403 ( 6) link_NAG-ASN : bond 0.00700 ( 10) link_NAG-ASN : angle 3.51726 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.955 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: A 323 MET cc_start: 0.8876 (tpp) cc_final: 0.8516 (tpp) REVERT: A 340 MET cc_start: 0.7054 (ppp) cc_final: 0.6619 (ppp) REVERT: B 218 MET cc_start: 0.9150 (tpp) cc_final: 0.8906 (tpp) REVERT: B 770 MET cc_start: 0.5790 (mmt) cc_final: 0.4713 (tpt) REVERT: C 316 MET cc_start: 0.7632 (tpt) cc_final: 0.7360 (tpt) REVERT: C 555 PHE cc_start: 0.7550 (m-80) cc_final: 0.7281 (m-80) REVERT: C 565 MET cc_start: 0.8589 (mmt) cc_final: 0.8164 (ptt) REVERT: D 89 PHE cc_start: 0.8938 (t80) cc_final: 0.8669 (t80) REVERT: D 229 ASP cc_start: 0.7768 (t70) cc_final: 0.7302 (t0) REVERT: D 276 MET cc_start: 0.8838 (ppp) cc_final: 0.8257 (ppp) REVERT: D 298 MET cc_start: 0.9116 (tpp) cc_final: 0.8842 (tmm) REVERT: D 340 MET cc_start: 0.8837 (tpt) cc_final: 0.8404 (tpt) REVERT: D 572 LEU cc_start: 0.9271 (tp) cc_final: 0.8841 (tp) REVERT: D 576 CYS cc_start: 0.8538 (t) cc_final: 0.8245 (m) REVERT: D 794 MET cc_start: 0.7684 (ptm) cc_final: 0.7457 (ptm) REVERT: D 796 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8487 (mt-10) outliers start: 2 outliers final: 0 residues processed: 259 average time/residue: 0.1404 time to fit residues: 61.3625 Evaluate side-chains 203 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.092980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067652 restraints weight = 96141.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.067326 restraints weight = 56242.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067674 restraints weight = 46245.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068606 restraints weight = 39096.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068668 restraints weight = 32863.160| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24123 Z= 0.212 Angle : 0.639 12.715 32686 Z= 0.320 Chirality : 0.043 0.342 3720 Planarity : 0.004 0.051 4096 Dihedral : 5.320 53.943 3440 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.04 % Allowed : 3.63 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 2929 helix: 0.49 (0.15), residues: 1242 sheet: -1.80 (0.27), residues: 359 loop : -1.61 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 431 TYR 0.018 0.002 TYR B 254 PHE 0.025 0.002 PHE C 153 TRP 0.024 0.001 TRP D 134 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00465 (24103) covalent geometry : angle 0.62987 (32634) SS BOND : bond 0.00183 ( 8) SS BOND : angle 0.68253 ( 16) hydrogen bonds : bond 0.03609 ( 924) hydrogen bonds : angle 4.99370 ( 2673) link_BETA1-4 : bond 0.00136 ( 2) link_BETA1-4 : angle 1.37274 ( 6) link_NAG-ASN : bond 0.00688 ( 10) link_NAG-ASN : angle 3.56668 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8895 (tpp) cc_final: 0.8531 (tpp) REVERT: A 340 MET cc_start: 0.7067 (ppp) cc_final: 0.6423 (ppp) REVERT: A 424 ILE cc_start: 0.6850 (mp) cc_final: 0.6639 (mp) REVERT: A 794 MET cc_start: 0.9092 (pmm) cc_final: 0.8684 (pmm) REVERT: B 218 MET cc_start: 0.9238 (tpp) cc_final: 0.8977 (tpp) REVERT: B 770 MET cc_start: 0.5701 (mmt) cc_final: 0.5207 (tpt) REVERT: C 316 MET cc_start: 0.7830 (tpt) cc_final: 0.7272 (tpp) REVERT: C 555 PHE cc_start: 0.7646 (m-80) cc_final: 0.7366 (m-80) REVERT: C 565 MET cc_start: 0.8589 (mmt) cc_final: 0.8159 (ptt) REVERT: D 89 PHE cc_start: 0.8964 (t80) cc_final: 0.8508 (t80) REVERT: D 229 ASP cc_start: 0.7910 (t70) cc_final: 0.7484 (t0) REVERT: D 247 MET cc_start: 0.8604 (tpp) cc_final: 0.8348 (tpp) REVERT: D 276 MET cc_start: 0.8873 (ppp) cc_final: 0.8239 (ppp) REVERT: D 298 MET cc_start: 0.9157 (tpp) cc_final: 0.8887 (tmm) REVERT: D 340 MET cc_start: 0.8880 (tpt) cc_final: 0.8461 (tpt) REVERT: D 565 MET cc_start: 0.9116 (mpp) cc_final: 0.8734 (mmt) REVERT: D 572 LEU cc_start: 0.9281 (tp) cc_final: 0.8842 (tp) REVERT: D 576 CYS cc_start: 0.8553 (t) cc_final: 0.8262 (m) REVERT: D 793 MET cc_start: 0.8708 (ptp) cc_final: 0.8398 (ptt) REVERT: D 794 MET cc_start: 0.7627 (ptm) cc_final: 0.7242 (ptm) REVERT: D 796 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8222 (mp0) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1411 time to fit residues: 60.2211 Evaluate side-chains 200 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 253 optimal weight: 0.3980 chunk 138 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 169 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 258 optimal weight: 2.9990 chunk 293 optimal weight: 0.0070 chunk 144 optimal weight: 30.0000 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 141 ASN C 654 ASN C 818 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.094730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066757 restraints weight = 96507.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068814 restraints weight = 51711.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070133 restraints weight = 34911.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.071033 restraints weight = 27131.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.071594 restraints weight = 22918.605| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24123 Z= 0.116 Angle : 0.611 9.394 32686 Z= 0.301 Chirality : 0.043 0.352 3720 Planarity : 0.003 0.056 4096 Dihedral : 5.165 55.615 3440 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.15), residues: 2929 helix: 0.50 (0.14), residues: 1237 sheet: -1.62 (0.26), residues: 366 loop : -1.59 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.039 0.001 TYR B 252 PHE 0.039 0.002 PHE D 735 TRP 0.021 0.001 TRP D 134 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00259 (24103) covalent geometry : angle 0.60250 (32634) SS BOND : bond 0.01258 ( 8) SS BOND : angle 0.81072 ( 16) hydrogen bonds : bond 0.03245 ( 924) hydrogen bonds : angle 4.75196 ( 2673) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 1.46385 ( 6) link_NAG-ASN : bond 0.00684 ( 10) link_NAG-ASN : angle 3.26757 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 MET cc_start: 0.6736 (ppp) cc_final: 0.6399 (ppp) REVERT: A 501 MET cc_start: 0.8129 (tpt) cc_final: 0.7907 (tpt) REVERT: A 576 CYS cc_start: 0.8115 (m) cc_final: 0.7908 (m) REVERT: A 794 MET cc_start: 0.9025 (pmm) cc_final: 0.8601 (pmm) REVERT: B 218 MET cc_start: 0.9153 (tpp) cc_final: 0.8900 (tpp) REVERT: B 360 MET cc_start: 0.8488 (tpp) cc_final: 0.7786 (mmm) REVERT: B 691 MET cc_start: 0.9114 (mmt) cc_final: 0.8772 (mmm) REVERT: B 770 MET cc_start: 0.5901 (mmt) cc_final: 0.5363 (tpt) REVERT: C 316 MET cc_start: 0.7595 (tpt) cc_final: 0.7116 (tpt) REVERT: C 555 PHE cc_start: 0.7477 (m-80) cc_final: 0.7161 (m-80) REVERT: C 565 MET cc_start: 0.8366 (mmt) cc_final: 0.8056 (ptt) REVERT: C 737 MET cc_start: 0.7623 (ppp) cc_final: 0.7327 (ppp) REVERT: C 770 MET cc_start: 0.8292 (mmm) cc_final: 0.8025 (mmm) REVERT: D 89 PHE cc_start: 0.8591 (t80) cc_final: 0.8323 (t80) REVERT: D 229 ASP cc_start: 0.7475 (t70) cc_final: 0.7042 (t0) REVERT: D 247 MET cc_start: 0.8513 (tpp) cc_final: 0.8262 (tpp) REVERT: D 276 MET cc_start: 0.8862 (ppp) cc_final: 0.8311 (ppp) REVERT: D 340 MET cc_start: 0.8684 (tpt) cc_final: 0.8360 (tpt) REVERT: D 565 MET cc_start: 0.9117 (mpp) cc_final: 0.8667 (mpp) REVERT: D 572 LEU cc_start: 0.9244 (tp) cc_final: 0.8755 (tp) REVERT: D 576 CYS cc_start: 0.8550 (t) cc_final: 0.8250 (m) REVERT: D 794 MET cc_start: 0.7550 (ptm) cc_final: 0.7273 (ptm) REVERT: D 796 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8515 (mt-10) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1378 time to fit residues: 62.8554 Evaluate side-chains 213 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 278 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 97 optimal weight: 0.0010 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 654 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.093989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.065747 restraints weight = 96455.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068411 restraints weight = 54366.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068801 restraints weight = 33769.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.069234 restraints weight = 27815.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069371 restraints weight = 26440.344| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24123 Z= 0.166 Angle : 0.625 10.393 32686 Z= 0.310 Chirality : 0.042 0.348 3720 Planarity : 0.004 0.055 4096 Dihedral : 5.178 53.690 3440 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 2929 helix: 0.57 (0.15), residues: 1240 sheet: -1.63 (0.27), residues: 361 loop : -1.59 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 280 TYR 0.029 0.001 TYR B 252 PHE 0.048 0.002 PHE D 735 TRP 0.023 0.001 TRP D 134 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00370 (24103) covalent geometry : angle 0.61675 (32634) SS BOND : bond 0.00284 ( 8) SS BOND : angle 0.61959 ( 16) hydrogen bonds : bond 0.03273 ( 924) hydrogen bonds : angle 4.80770 ( 2673) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 1.43097 ( 6) link_NAG-ASN : bond 0.00649 ( 10) link_NAG-ASN : angle 3.36536 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.9709 (mm) cc_final: 0.9492 (mm) REVERT: A 340 MET cc_start: 0.6948 (ppp) cc_final: 0.6520 (ppp) REVERT: A 576 CYS cc_start: 0.8212 (m) cc_final: 0.8001 (m) REVERT: B 218 MET cc_start: 0.9154 (tpp) cc_final: 0.8949 (tpp) REVERT: B 252 TYR cc_start: 0.8998 (m-80) cc_final: 0.8766 (m-10) REVERT: B 298 MET cc_start: 0.8780 (mtm) cc_final: 0.8373 (mpp) REVERT: B 770 MET cc_start: 0.5645 (mmt) cc_final: 0.5113 (tpt) REVERT: C 42 PHE cc_start: 0.8062 (m-80) cc_final: 0.7844 (m-80) REVERT: C 316 MET cc_start: 0.7835 (tpt) cc_final: 0.7249 (tpp) REVERT: C 555 PHE cc_start: 0.7567 (m-80) cc_final: 0.7222 (m-80) REVERT: C 565 MET cc_start: 0.8514 (mmt) cc_final: 0.8109 (ptt) REVERT: C 687 ASP cc_start: 0.6835 (m-30) cc_final: 0.6619 (m-30) REVERT: D 229 ASP cc_start: 0.7580 (t70) cc_final: 0.7182 (t0) REVERT: D 247 MET cc_start: 0.8595 (tpp) cc_final: 0.8333 (tpp) REVERT: D 276 MET cc_start: 0.8945 (ppp) cc_final: 0.8369 (ppp) REVERT: D 298 MET cc_start: 0.9115 (tpp) cc_final: 0.8852 (tmm) REVERT: D 340 MET cc_start: 0.8794 (tpt) cc_final: 0.8337 (tpt) REVERT: D 572 LEU cc_start: 0.9292 (tp) cc_final: 0.8843 (tp) REVERT: D 576 CYS cc_start: 0.8542 (t) cc_final: 0.8251 (m) REVERT: D 794 MET cc_start: 0.7707 (ptm) cc_final: 0.7444 (ptm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1362 time to fit residues: 61.2633 Evaluate side-chains 208 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 267 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 251 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 245 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 654 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065498 restraints weight = 96458.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.067520 restraints weight = 51936.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.068822 restraints weight = 35184.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069616 restraints weight = 27427.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070213 restraints weight = 23406.739| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24123 Z= 0.157 Angle : 0.634 10.335 32686 Z= 0.312 Chirality : 0.043 0.351 3720 Planarity : 0.004 0.070 4096 Dihedral : 5.216 53.740 3440 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 2929 helix: 0.59 (0.15), residues: 1241 sheet: -1.64 (0.27), residues: 360 loop : -1.63 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 775 TYR 0.026 0.001 TYR B 252 PHE 0.045 0.002 PHE D 735 TRP 0.025 0.001 TRP D 134 HIS 0.005 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00353 (24103) covalent geometry : angle 0.62618 (32634) SS BOND : bond 0.00200 ( 8) SS BOND : angle 0.50477 ( 16) hydrogen bonds : bond 0.03221 ( 924) hydrogen bonds : angle 4.77738 ( 2673) link_BETA1-4 : bond 0.00106 ( 2) link_BETA1-4 : angle 1.38147 ( 6) link_NAG-ASN : bond 0.00638 ( 10) link_NAG-ASN : angle 3.35226 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.915 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 322 LEU cc_start: 0.9650 (mm) cc_final: 0.9449 (mm) REVERT: A 323 MET cc_start: 0.9078 (tpp) cc_final: 0.8456 (tpp) REVERT: A 340 MET cc_start: 0.6799 (ppp) cc_final: 0.6406 (ppp) REVERT: A 691 MET cc_start: 0.9017 (ptp) cc_final: 0.8345 (pmm) REVERT: A 794 MET cc_start: 0.9052 (pmm) cc_final: 0.8701 (pmm) REVERT: B 218 MET cc_start: 0.9134 (tpp) cc_final: 0.8927 (tpp) REVERT: B 770 MET cc_start: 0.5882 (mmt) cc_final: 0.5351 (tpt) REVERT: C 152 ASP cc_start: 0.8713 (t0) cc_final: 0.8491 (t0) REVERT: C 316 MET cc_start: 0.7820 (tpt) cc_final: 0.7259 (tpp) REVERT: C 555 PHE cc_start: 0.7516 (m-80) cc_final: 0.7161 (m-80) REVERT: C 565 MET cc_start: 0.8401 (mmt) cc_final: 0.8059 (ptt) REVERT: C 737 MET cc_start: 0.7593 (ppp) cc_final: 0.7280 (ppp) REVERT: C 770 MET cc_start: 0.8264 (mmm) cc_final: 0.8034 (mmm) REVERT: D 89 PHE cc_start: 0.8528 (t80) cc_final: 0.8252 (t80) REVERT: D 229 ASP cc_start: 0.7618 (t70) cc_final: 0.7219 (t0) REVERT: D 247 MET cc_start: 0.8526 (tpp) cc_final: 0.8323 (tpp) REVERT: D 276 MET cc_start: 0.8953 (ppp) cc_final: 0.8343 (ppp) REVERT: D 298 MET cc_start: 0.8929 (tpp) cc_final: 0.8683 (tmm) REVERT: D 340 MET cc_start: 0.8744 (tpt) cc_final: 0.8185 (tpt) REVERT: D 565 MET cc_start: 0.9097 (mpp) cc_final: 0.8715 (mmt) REVERT: D 572 LEU cc_start: 0.9258 (tp) cc_final: 0.8771 (tp) REVERT: D 576 CYS cc_start: 0.8601 (t) cc_final: 0.8297 (m) REVERT: D 794 MET cc_start: 0.7652 (ptm) cc_final: 0.7272 (ptm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1382 time to fit residues: 61.7271 Evaluate side-chains 210 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 267 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 200 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 27 optimal weight: 0.0050 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.094296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066658 restraints weight = 97292.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.069326 restraints weight = 56229.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069715 restraints weight = 33723.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070153 restraints weight = 27752.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070307 restraints weight = 26926.849| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24123 Z= 0.138 Angle : 0.632 9.663 32686 Z= 0.310 Chirality : 0.043 0.354 3720 Planarity : 0.004 0.056 4096 Dihedral : 5.201 53.970 3440 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 2929 helix: 0.57 (0.15), residues: 1241 sheet: -1.61 (0.27), residues: 360 loop : -1.62 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 775 TYR 0.024 0.001 TYR A 176 PHE 0.044 0.002 PHE D 735 TRP 0.026 0.001 TRP D 134 HIS 0.004 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00313 (24103) covalent geometry : angle 0.62372 (32634) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.47301 ( 16) hydrogen bonds : bond 0.03168 ( 924) hydrogen bonds : angle 4.75137 ( 2673) link_BETA1-4 : bond 0.00189 ( 2) link_BETA1-4 : angle 1.45479 ( 6) link_NAG-ASN : bond 0.00664 ( 10) link_NAG-ASN : angle 3.30968 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.599 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 340 MET cc_start: 0.6954 (ppp) cc_final: 0.6496 (ppp) REVERT: A 691 MET cc_start: 0.9031 (ptp) cc_final: 0.8367 (pmm) REVERT: A 794 MET cc_start: 0.9086 (pmm) cc_final: 0.8720 (pmm) REVERT: B 770 MET cc_start: 0.5628 (mmt) cc_final: 0.5110 (tpt) REVERT: C 152 ASP cc_start: 0.8638 (t0) cc_final: 0.8435 (t0) REVERT: C 316 MET cc_start: 0.7809 (tpt) cc_final: 0.7222 (tpp) REVERT: C 555 PHE cc_start: 0.7631 (m-80) cc_final: 0.7250 (m-80) REVERT: C 565 MET cc_start: 0.8525 (mmt) cc_final: 0.8101 (ptt) REVERT: C 737 MET cc_start: 0.7681 (ppp) cc_final: 0.7371 (ppp) REVERT: D 89 PHE cc_start: 0.8617 (t80) cc_final: 0.8368 (t80) REVERT: D 229 ASP cc_start: 0.7617 (t70) cc_final: 0.7125 (t0) REVERT: D 276 MET cc_start: 0.8920 (ppp) cc_final: 0.8397 (ppp) REVERT: D 298 MET cc_start: 0.9095 (tpp) cc_final: 0.8826 (tmm) REVERT: D 340 MET cc_start: 0.8793 (tpt) cc_final: 0.8152 (tpt) REVERT: D 565 MET cc_start: 0.9098 (mpp) cc_final: 0.8726 (mmt) REVERT: D 572 LEU cc_start: 0.9274 (tp) cc_final: 0.8804 (tp) REVERT: D 576 CYS cc_start: 0.8501 (t) cc_final: 0.8162 (m) REVERT: D 737 MET cc_start: 0.8441 (mpp) cc_final: 0.8178 (mpp) REVERT: D 794 MET cc_start: 0.7715 (ptm) cc_final: 0.7353 (ptm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1322 time to fit residues: 58.9902 Evaluate side-chains 206 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 217 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 291 optimal weight: 0.2980 chunk 287 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.095290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.067328 restraints weight = 96561.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069433 restraints weight = 51490.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070767 restraints weight = 34698.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071639 restraints weight = 26880.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.072239 restraints weight = 22731.620| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24123 Z= 0.115 Angle : 0.645 11.531 32686 Z= 0.311 Chirality : 0.043 0.357 3720 Planarity : 0.004 0.056 4096 Dihedral : 5.133 55.699 3440 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2929 helix: 0.65 (0.15), residues: 1227 sheet: -1.57 (0.27), residues: 356 loop : -1.63 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 775 TYR 0.019 0.001 TYR B 324 PHE 0.043 0.002 PHE D 735 TRP 0.023 0.001 TRP D 134 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00263 (24103) covalent geometry : angle 0.63836 (32634) SS BOND : bond 0.00134 ( 8) SS BOND : angle 0.44522 ( 16) hydrogen bonds : bond 0.03057 ( 924) hydrogen bonds : angle 4.66980 ( 2673) link_BETA1-4 : bond 0.00146 ( 2) link_BETA1-4 : angle 1.42317 ( 6) link_NAG-ASN : bond 0.00692 ( 10) link_NAG-ASN : angle 3.18401 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.952 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 340 MET cc_start: 0.6609 (ppp) cc_final: 0.6215 (ppp) REVERT: A 576 CYS cc_start: 0.8173 (m) cc_final: 0.7967 (m) REVERT: A 691 MET cc_start: 0.8968 (ptp) cc_final: 0.8332 (pmm) REVERT: A 794 MET cc_start: 0.9036 (pmm) cc_final: 0.8685 (pmm) REVERT: B 709 MET cc_start: 0.7584 (ppp) cc_final: 0.7123 (ppp) REVERT: B 770 MET cc_start: 0.5764 (mmt) cc_final: 0.5207 (tpt) REVERT: C 156 LEU cc_start: 0.9147 (pp) cc_final: 0.8431 (tt) REVERT: C 316 MET cc_start: 0.7791 (tpt) cc_final: 0.7548 (tpt) REVERT: C 555 PHE cc_start: 0.7524 (m-80) cc_final: 0.7191 (m-80) REVERT: C 565 MET cc_start: 0.8362 (mmt) cc_final: 0.7986 (ptt) REVERT: C 737 MET cc_start: 0.7631 (ppp) cc_final: 0.7326 (ppp) REVERT: C 770 MET cc_start: 0.8216 (mmm) cc_final: 0.7638 (mmt) REVERT: D 89 PHE cc_start: 0.8496 (t80) cc_final: 0.8259 (t80) REVERT: D 229 ASP cc_start: 0.7580 (t70) cc_final: 0.7203 (t0) REVERT: D 276 MET cc_start: 0.8897 (ppp) cc_final: 0.8355 (ppp) REVERT: D 298 MET cc_start: 0.8846 (tpp) cc_final: 0.8596 (tmm) REVERT: D 340 MET cc_start: 0.8659 (tpt) cc_final: 0.8017 (tpt) REVERT: D 534 MET cc_start: 0.8257 (ppp) cc_final: 0.7482 (ppp) REVERT: D 535 THR cc_start: 0.8960 (p) cc_final: 0.8699 (p) REVERT: D 565 MET cc_start: 0.9086 (mpp) cc_final: 0.8700 (mmt) REVERT: D 572 LEU cc_start: 0.9217 (tp) cc_final: 0.8685 (tp) REVERT: D 576 CYS cc_start: 0.8583 (t) cc_final: 0.8223 (m) REVERT: D 737 MET cc_start: 0.8451 (mpp) cc_final: 0.8096 (mpp) REVERT: D 794 MET cc_start: 0.7468 (ptm) cc_final: 0.7100 (ptm) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1349 time to fit residues: 64.4216 Evaluate side-chains 218 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 238 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 654 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.093361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065204 restraints weight = 97298.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067224 restraints weight = 52474.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068507 restraints weight = 35567.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.069338 restraints weight = 27772.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069865 restraints weight = 23660.803| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24123 Z= 0.180 Angle : 0.666 13.890 32686 Z= 0.329 Chirality : 0.043 0.352 3720 Planarity : 0.004 0.055 4096 Dihedral : 5.241 53.680 3440 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 2929 helix: 0.63 (0.15), residues: 1235 sheet: -1.64 (0.27), residues: 355 loop : -1.59 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 775 TYR 0.021 0.001 TYR A 176 PHE 0.046 0.002 PHE D 735 TRP 0.032 0.001 TRP D 134 HIS 0.025 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00400 (24103) covalent geometry : angle 0.65784 (32634) SS BOND : bond 0.00171 ( 8) SS BOND : angle 0.52629 ( 16) hydrogen bonds : bond 0.03245 ( 924) hydrogen bonds : angle 4.80785 ( 2673) link_BETA1-4 : bond 0.00186 ( 2) link_BETA1-4 : angle 1.37360 ( 6) link_NAG-ASN : bond 0.00623 ( 10) link_NAG-ASN : angle 3.36434 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3941.95 seconds wall clock time: 69 minutes 19.19 seconds (4159.19 seconds total)