Starting phenix.real_space_refine on Fri Sep 19 09:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eos_31229/09_2025/7eos_31229.map" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 15760 2.51 5 N 4120 2.21 5 O 4570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24600 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6007 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 6167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6167 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 32, 'TRANS': 756} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "A" 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.24, per 1000 atoms: 0.25 Number of scatterers: 24600 At special positions: 0 Unit cell: (120.91, 148.73, 188.32, 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 150 16.00 O 4570 8.00 N 4120 7.00 C 15760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 745 " - pdb=" SG CYS A 800 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 800 " distance=2.03 Simple disulfide: pdb=" SG CYS D 79 " - pdb=" SG CYS D 308 " distance=2.04 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 744 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 NAG-ASN " NAG A 901 " - " ASN A 340 " " NAG A 902 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 368 " " NAG B 904 " - " ASN B 471 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 203 " " NAG B 907 " - " ASN B 239 " " NAG C 901 " - " ASN C 340 " " NAG C 902 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 368 " " NAG D 904 " - " ASN D 471 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 203 " " NAG D 907 " - " ASN D 239 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 24 sheets defined 42.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.657A pdb=" N ARG A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 106 through 121 removed outlier: 4.473A pdb=" N ALA A 110 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.773A pdb=" N VAL A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 Processing helix chain 'A' and resid 459 through 472 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 515 through 522 removed outlier: 4.130A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 579 removed outlier: 4.057A pdb=" N VAL A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.791A pdb=" N TRP A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 653 Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.817A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 removed outlier: 3.739A pdb=" N TYR A 676 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.906A pdb=" N LYS A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 770 through 786 removed outlier: 4.596A pdb=" N GLN A 774 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.131A pdb=" N ALA A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 52 Processing helix chain 'B' and resid 70 through 83 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.675A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.098A pdb=" N VAL B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 256 through 262 removed outlier: 4.251A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.022A pdb=" N GLU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.894A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 560 through 584 Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 657 removed outlier: 3.614A pdb=" N ILE B 631 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.059A pdb=" N ARG B 704 " --> pdb=" O SER B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.986A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.792A pdb=" N ARG B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 843 removed outlier: 3.559A pdb=" N HIS B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 56 removed outlier: 3.533A pdb=" N ARG C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.616A pdb=" N GLN C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 116 " --> pdb=" O MET C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.817A pdb=" N VAL C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 Processing helix chain 'C' and resid 459 through 472 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 515 through 522 removed outlier: 4.115A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 579 removed outlier: 4.034A pdb=" N VAL C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.784A pdb=" N TRP C 609 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.806A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 676 removed outlier: 3.730A pdb=" N TYR C 676 " --> pdb=" O PRO C 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 688 through 698 removed outlier: 4.004A pdb=" N ARG C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 708 removed outlier: 3.902A pdb=" N LYS C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 732 through 741 Processing helix chain 'C' and resid 770 through 786 removed outlier: 4.570A pdb=" N GLN C 774 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 796 Processing helix chain 'C' and resid 814 through 837 removed outlier: 4.142A pdb=" N ALA C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 823 " --> pdb=" O GLY C 819 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 825 " --> pdb=" O PHE C 821 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 52 Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.653A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 146 through 159 removed outlier: 4.078A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 256 through 262 removed outlier: 4.260A pdb=" N ARG D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 296 Processing helix chain 'D' and resid 317 through 327 Processing helix chain 'D' and resid 381 through 385 removed outlier: 4.028A pdb=" N GLU D 385 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.901A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 584 Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 657 removed outlier: 3.677A pdb=" N ILE D 631 " --> pdb=" O PHE D 627 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 642 " --> pdb=" O GLY D 638 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 695 Processing helix chain 'D' and resid 700 through 707 removed outlier: 4.048A pdb=" N ARG D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.988A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.784A pdb=" N ARG D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 843 removed outlier: 3.566A pdb=" N HIS D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 6.738A pdb=" N ASN A 35 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 99 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 125 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 100 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE A 124 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 205 removed outlier: 6.259A pdb=" N LEU A 172 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 256 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 229 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 373 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.927A pdb=" N ASP A 523 " --> pdb=" O LEU A 765 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 417 through 420 removed outlier: 3.818A pdb=" N CYS A 455 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 450 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 440 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 438 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AA6, first strand: chain 'A' and resid 682 through 683 removed outlier: 6.374A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 537 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 748 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.057A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.527A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 164 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 220 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 271 removed outlier: 4.286A pdb=" N GLY B 365 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 355 " --> pdb=" O GLN B 363 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLN B 363 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLN B 357 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU B 361 " --> pdb=" O GLN B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 402 removed outlier: 3.675A pdb=" N LEU B 398 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 475 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE B 435 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU B 478 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR B 437 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 488 removed outlier: 4.558A pdb=" N GLU B 497 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 681 through 682 removed outlier: 3.999A pdb=" N ALA B 682 " --> pdb=" O ALA B 728 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE B 730 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLN B 536 " --> pdb=" O PHE B 753 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE B 753 " --> pdb=" O GLN B 536 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 538 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU B 751 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 540 " --> pdb=" O THR B 749 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 747 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 68 through 72 removed outlier: 6.696A pdb=" N ASN C 35 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 99 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA C 37 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 125 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 124 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 204 through 205 removed outlier: 6.250A pdb=" N LEU C 172 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 256 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 229 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 373 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 478 through 479 removed outlier: 3.930A pdb=" N ASP C 523 " --> pdb=" O LEU C 765 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 420 removed outlier: 3.817A pdb=" N CYS C 455 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 450 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 440 " --> pdb=" O MET C 450 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 438 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AB9, first strand: chain 'C' and resid 682 through 683 removed outlier: 6.371A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 537 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 748 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 61 through 66 removed outlier: 3.937A pdb=" N ILE D 29 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.562A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 164 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 220 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 271 removed outlier: 4.299A pdb=" N GLY D 365 " --> pdb=" O ILE D 353 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 355 " --> pdb=" O GLN D 363 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN D 363 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN D 357 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU D 361 " --> pdb=" O GLN D 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 397 through 402 removed outlier: 3.691A pdb=" N LEU D 398 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 475 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE D 435 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU D 478 " --> pdb=" O ILE D 435 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 487 through 488 removed outlier: 4.500A pdb=" N GLU D 497 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 681 through 682 removed outlier: 3.997A pdb=" N ALA D 682 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 730 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N GLN D 536 " --> pdb=" O PHE D 753 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE D 753 " --> pdb=" O GLN D 536 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 540 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 747 " --> pdb=" O VAL D 542 " (cutoff:3.500A) 982 hydrogen bonds defined for protein. 2892 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: 4.96 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7858 1.34 - 1.46: 5880 1.46 - 1.58: 11160 1.58 - 1.70: 0 1.70 - 1.81: 256 Bond restraints: 25154 Sorted by residual: bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 NAG B 904 " pdb=" O5 NAG B 904 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 25149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 33559 1.36 - 2.73: 437 2.73 - 4.09: 88 4.09 - 5.46: 16 5.46 - 6.82: 12 Bond angle restraints: 34112 Sorted by residual: angle pdb=" C MET D 394 " pdb=" N SER D 395 " pdb=" CA SER D 395 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.53e+00 angle pdb=" C MET B 394 " pdb=" N SER B 395 " pdb=" CA SER B 395 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.46e+00 angle pdb=" C GLY C 41 " pdb=" N HIS C 42 " pdb=" CA HIS C 42 " ideal model delta sigma weight residual 122.46 125.22 -2.76 1.41e+00 5.03e-01 3.82e+00 angle pdb=" CA LEU C 89 " pdb=" CB LEU C 89 " pdb=" CG LEU C 89 " ideal model delta sigma weight residual 116.30 123.12 -6.82 3.50e+00 8.16e-02 3.80e+00 angle pdb=" N GLN C 661 " pdb=" CA GLN C 661 " pdb=" C GLN C 661 " ideal model delta sigma weight residual 112.93 110.34 2.59 1.33e+00 5.65e-01 3.80e+00 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 14756 22.93 - 45.86: 386 45.86 - 68.79: 39 68.79 - 91.72: 1 91.72 - 114.65: 6 Dihedral angle restraints: 15188 sinusoidal: 6194 harmonic: 8994 Sorted by residual: dihedral pdb=" C1 NAG B 901 " pdb=" C5 NAG B 901 " pdb=" O5 NAG B 901 " pdb=" C4 NAG B 901 " ideal model delta sinusoidal sigma weight residual -64.11 50.54 -114.65 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 NAG D 901 " pdb=" C5 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C6 NAG D 901 " ideal model delta sinusoidal sigma weight residual 171.16 -74.25 -114.59 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 NAG D 901 " pdb=" C5 NAG D 901 " pdb=" O5 NAG D 901 " pdb=" C4 NAG D 901 " ideal model delta sinusoidal sigma weight residual -64.11 50.47 -114.58 1 3.00e+01 1.11e-03 1.51e+01 ... (remaining 15185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3302 0.055 - 0.109: 533 0.109 - 0.164: 69 0.164 - 0.219: 0 0.219 - 0.274: 2 Chirality restraints: 3906 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 340 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG D 901 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG D 901 " pdb=" O5 NAG D 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 3903 not shown) Planarity restraints: 4314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 390 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 391 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 390 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO C 391 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 139 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 140 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.015 5.00e-02 4.00e+02 ... (remaining 4311 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5191 2.78 - 3.31: 24365 3.31 - 3.84: 39025 3.84 - 4.37: 42673 4.37 - 4.90: 74695 Nonbonded interactions: 185949 Sorted by model distance: nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.254 3.040 nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.263 3.040 nonbonded pdb=" O GLU D 80 " pdb=" OG SER D 84 " model vdw 2.270 3.040 nonbonded pdb=" O GLU B 80 " pdb=" OG SER B 84 " model vdw 2.278 3.040 nonbonded pdb=" O PHE C 680 " pdb=" OH TYR C 704 " model vdw 2.285 3.040 ... (remaining 185944 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.610 Find NCS groups from input model: 0.470 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: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 0.082 25190 Z= 0.106 Angle : 0.428 8.573 34202 Z= 0.208 Chirality : 0.041 0.274 3906 Planarity : 0.002 0.031 4296 Dihedral : 9.752 114.648 9326 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 1.89 % Allowed : 6.63 % Favored : 91.48 % 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 aren not related in a simple way. whole: 0.47 (0.16), residues: 3066 helix: 1.89 (0.15), residues: 1262 sheet: 0.46 (0.29), residues: 372 loop : -1.24 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 293 TYR 0.007 0.001 TYR C 737 PHE 0.008 0.001 PHE C 652 TRP 0.005 0.000 TRP C 378 HIS 0.001 0.000 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00203 (25154) covalent geometry : angle 0.42109 (34112) SS BOND : bond 0.00195 ( 18) SS BOND : angle 0.38694 ( 36) hydrogen bonds : bond 0.14263 ( 982) hydrogen bonds : angle 5.91069 ( 2892) link_NAG-ASN : bond 0.00558 ( 18) link_NAG-ASN : angle 1.98377 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 351 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8688 (mtt) cc_final: 0.8277 (mtm) REVERT: A 183 PHE cc_start: 0.6256 (m-10) cc_final: 0.5759 (m-80) REVERT: A 331 MET cc_start: 0.4303 (ttt) cc_final: 0.2919 (tpp) REVERT: A 389 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6173 (t) REVERT: A 396 PHE cc_start: 0.5997 (m-80) cc_final: 0.5767 (m-80) REVERT: A 817 MET cc_start: 0.4901 (mpp) cc_final: 0.4205 (ptt) REVERT: B 343 ASP cc_start: 0.8489 (m-30) cc_final: 0.8190 (p0) REVERT: B 639 PHE cc_start: 0.8312 (t80) cc_final: 0.7917 (t80) REVERT: B 706 MET cc_start: 0.8462 (mtm) cc_final: 0.8014 (mtp) REVERT: B 813 MET cc_start: 0.7733 (mpp) cc_final: 0.7495 (ppp) REVERT: C 158 MET cc_start: 0.8692 (mtt) cc_final: 0.8301 (mtm) REVERT: C 320 CYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3946 (p) REVERT: C 331 MET cc_start: 0.3982 (ttt) cc_final: 0.2655 (tpp) REVERT: C 380 ASN cc_start: 0.7490 (p0) cc_final: 0.7235 (p0) REVERT: C 389 VAL cc_start: 0.6552 (OUTLIER) cc_final: 0.6070 (t) REVERT: C 396 PHE cc_start: 0.6139 (m-80) cc_final: 0.5835 (m-80) REVERT: C 637 PHE cc_start: 0.8642 (t80) cc_final: 0.8092 (m-10) REVERT: C 817 MET cc_start: 0.4881 (mpp) cc_final: 0.4338 (ptt) REVERT: C 828 MET cc_start: 0.8604 (tpp) cc_final: 0.8279 (mtt) REVERT: D 237 MET cc_start: 0.8884 (tmm) cc_final: 0.8667 (tmm) REVERT: D 343 ASP cc_start: 0.8476 (m-30) cc_final: 0.8145 (p0) REVERT: D 762 MET cc_start: 0.8224 (mtm) cc_final: 0.7850 (mtp) outliers start: 50 outliers final: 15 residues processed: 398 average time/residue: 0.1696 time to fit residues: 106.2417 Evaluate side-chains 232 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 367 ASN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 GLN B 477 HIS C 766 GLN D 477 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.075009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.057009 restraints weight = 146192.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.058504 restraints weight = 82420.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.059462 restraints weight = 56787.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.060080 restraints weight = 44756.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.060521 restraints weight = 38223.465| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25190 Z= 0.181 Angle : 0.605 12.506 34202 Z= 0.301 Chirality : 0.044 0.269 3906 Planarity : 0.004 0.035 4296 Dihedral : 6.841 90.598 3714 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 2.23 % Allowed : 9.96 % Favored : 87.80 % 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 aren not related in a simple way. whole: 0.30 (0.16), residues: 3066 helix: 1.76 (0.15), residues: 1258 sheet: 0.05 (0.27), residues: 398 loop : -1.23 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 392 TYR 0.017 0.002 TYR C 180 PHE 0.024 0.002 PHE A 115 TRP 0.027 0.001 TRP C 55 HIS 0.007 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00398 (25154) covalent geometry : angle 0.59835 (34112) SS BOND : bond 0.00692 ( 18) SS BOND : angle 0.88730 ( 36) hydrogen bonds : bond 0.03248 ( 982) hydrogen bonds : angle 4.69058 ( 2892) link_NAG-ASN : bond 0.00698 ( 18) link_NAG-ASN : angle 2.27318 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.6281 (tpp) cc_final: 0.5931 (tpp) REVERT: A 817 MET cc_start: 0.4901 (mpp) cc_final: 0.4103 (ptt) REVERT: B 155 MET cc_start: 0.9307 (mtp) cc_final: 0.9057 (mtp) REVERT: B 343 ASP cc_start: 0.8303 (m-30) cc_final: 0.8008 (p0) REVERT: B 706 MET cc_start: 0.8758 (mtm) cc_final: 0.8542 (mtp) REVERT: B 813 MET cc_start: 0.7208 (mpp) cc_final: 0.6907 (tmm) REVERT: C 200 MET cc_start: 0.6221 (tpp) cc_final: 0.5862 (tpp) REVERT: C 320 CYS cc_start: 0.4483 (OUTLIER) cc_final: 0.3868 (p) REVERT: C 637 PHE cc_start: 0.8683 (t80) cc_final: 0.8164 (m-80) REVERT: C 817 MET cc_start: 0.4694 (mpp) cc_final: 0.4330 (mtm) REVERT: C 823 MET cc_start: 0.8475 (ppp) cc_final: 0.8250 (ppp) REVERT: C 828 MET cc_start: 0.8563 (tpp) cc_final: 0.8222 (mtt) REVERT: D 326 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8402 (ttt) REVERT: D 754 PHE cc_start: 0.7355 (m-80) cc_final: 0.7155 (m-80) outliers start: 59 outliers final: 30 residues processed: 249 average time/residue: 0.1589 time to fit residues: 63.9963 Evaluate side-chains 208 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 652 PHE Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 72 optimal weight: 0.0980 chunk 109 optimal weight: 0.1980 chunk 264 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 285 optimal weight: 40.0000 chunk 143 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 302 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 HIS ** D 536 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 = 0.3794 r_free = 0.3794 target = 0.075659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.057461 restraints weight = 145123.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.058971 restraints weight = 81334.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.059951 restraints weight = 56097.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060587 restraints weight = 44070.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061054 restraints weight = 37503.661| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25190 Z= 0.100 Angle : 0.542 11.052 34202 Z= 0.264 Chirality : 0.042 0.269 3906 Planarity : 0.003 0.031 4296 Dihedral : 6.187 75.390 3712 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 2.23 % Allowed : 10.64 % Favored : 87.12 % 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 aren not related in a simple way. whole: 0.25 (0.16), residues: 3066 helix: 1.67 (0.15), residues: 1260 sheet: 0.06 (0.27), residues: 396 loop : -1.23 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 694 TYR 0.018 0.001 TYR C 281 PHE 0.034 0.001 PHE C 183 TRP 0.008 0.001 TRP C 55 HIS 0.007 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00218 (25154) covalent geometry : angle 0.53317 (34112) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.78621 ( 36) hydrogen bonds : bond 0.02883 ( 982) hydrogen bonds : angle 4.47012 ( 2892) link_NAG-ASN : bond 0.00583 ( 18) link_NAG-ASN : angle 2.39898 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 HIS cc_start: 0.8675 (OUTLIER) cc_final: 0.8473 (m170) REVERT: A 817 MET cc_start: 0.4880 (mpp) cc_final: 0.4152 (mtm) REVERT: A 823 MET cc_start: 0.8177 (ppp) cc_final: 0.7966 (ppp) REVERT: B 155 MET cc_start: 0.9322 (mtp) cc_final: 0.9097 (mtp) REVERT: B 343 ASP cc_start: 0.8304 (m-30) cc_final: 0.7984 (p0) REVERT: B 706 MET cc_start: 0.8611 (mtm) cc_final: 0.8403 (mtp) REVERT: C 200 MET cc_start: 0.6202 (tpp) cc_final: 0.5754 (tpp) REVERT: C 320 CYS cc_start: 0.4259 (OUTLIER) cc_final: 0.3653 (p) REVERT: C 637 PHE cc_start: 0.8642 (t80) cc_final: 0.8110 (m-80) REVERT: C 653 MET cc_start: 0.7419 (mmm) cc_final: 0.7194 (mmm) REVERT: C 817 MET cc_start: 0.4540 (mpp) cc_final: 0.4265 (mtm) REVERT: C 828 MET cc_start: 0.8550 (tpp) cc_final: 0.8213 (mtt) REVERT: D 326 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8432 (ttt) outliers start: 59 outliers final: 30 residues processed: 231 average time/residue: 0.1514 time to fit residues: 56.9939 Evaluate side-chains 206 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 652 PHE Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 161 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 280 optimal weight: 0.1980 chunk 237 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.074391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056013 restraints weight = 147018.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.057425 restraints weight = 84746.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.058360 restraints weight = 59724.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.058933 restraints weight = 47584.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.059229 restraints weight = 41311.382| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25190 Z= 0.130 Angle : 0.558 11.289 34202 Z= 0.276 Chirality : 0.042 0.272 3906 Planarity : 0.003 0.032 4296 Dihedral : 5.303 58.266 3711 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 2.08 % Allowed : 10.76 % Favored : 87.16 % 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 aren not related in a simple way. whole: 0.17 (0.16), residues: 3066 helix: 1.64 (0.15), residues: 1256 sheet: -0.21 (0.26), residues: 454 loop : -1.26 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 392 TYR 0.015 0.001 TYR C 165 PHE 0.051 0.001 PHE A 183 TRP 0.007 0.001 TRP C 771 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00290 (25154) covalent geometry : angle 0.54618 (34112) SS BOND : bond 0.00276 ( 18) SS BOND : angle 0.91814 ( 36) hydrogen bonds : bond 0.02904 ( 982) hydrogen bonds : angle 4.40095 ( 2892) link_NAG-ASN : bond 0.00561 ( 18) link_NAG-ASN : angle 2.87088 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.8850 (tpp) cc_final: 0.8556 (tpp) REVERT: A 119 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8523 (m170) REVERT: A 817 MET cc_start: 0.5093 (mpp) cc_final: 0.4413 (mtm) REVERT: B 354 MET cc_start: 0.8123 (tpp) cc_final: 0.7809 (tpp) REVERT: C 200 MET cc_start: 0.6503 (tpp) cc_final: 0.5990 (tpp) REVERT: C 320 CYS cc_start: 0.4631 (OUTLIER) cc_final: 0.4011 (p) REVERT: C 637 PHE cc_start: 0.8653 (t80) cc_final: 0.8110 (m-80) REVERT: C 828 MET cc_start: 0.8522 (tpp) cc_final: 0.8218 (mtt) REVERT: D 326 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8300 (ttt) outliers start: 55 outliers final: 34 residues processed: 221 average time/residue: 0.1547 time to fit residues: 56.8157 Evaluate side-chains 201 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 299 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 291 optimal weight: 0.6980 chunk 35 optimal weight: 0.0870 chunk 279 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS B 536 GLN ** D 536 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 = 0.3750 r_free = 0.3750 target = 0.073848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.055353 restraints weight = 146066.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.056764 restraints weight = 84296.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.057688 restraints weight = 59371.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.058232 restraints weight = 47338.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.058539 restraints weight = 41249.681| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25190 Z= 0.124 Angle : 0.557 11.923 34202 Z= 0.275 Chirality : 0.042 0.275 3906 Planarity : 0.003 0.031 4296 Dihedral : 4.997 59.627 3710 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 1.97 % Allowed : 11.55 % Favored : 86.48 % 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 aren not related in a simple way. whole: 0.12 (0.16), residues: 3066 helix: 1.62 (0.15), residues: 1256 sheet: -0.29 (0.26), residues: 454 loop : -1.29 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 694 TYR 0.013 0.001 TYR B 692 PHE 0.051 0.001 PHE A 183 TRP 0.007 0.001 TRP B 151 HIS 0.016 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00275 (25154) covalent geometry : angle 0.54705 (34112) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.88222 ( 36) hydrogen bonds : bond 0.02830 ( 982) hydrogen bonds : angle 4.30964 ( 2892) link_NAG-ASN : bond 0.00556 ( 18) link_NAG-ASN : angle 2.57356 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.8939 (tpp) cc_final: 0.8593 (tpp) REVERT: A 200 MET cc_start: 0.6594 (tpp) cc_final: 0.6066 (tpp) REVERT: A 817 MET cc_start: 0.5103 (mpp) cc_final: 0.4611 (mtm) REVERT: B 354 MET cc_start: 0.8130 (tpp) cc_final: 0.7585 (tpp) REVERT: C 200 MET cc_start: 0.6627 (tpp) cc_final: 0.6165 (tpp) REVERT: C 320 CYS cc_start: 0.4338 (OUTLIER) cc_final: 0.3844 (p) REVERT: C 637 PHE cc_start: 0.8615 (t80) cc_final: 0.8083 (m-80) REVERT: C 828 MET cc_start: 0.8509 (tpp) cc_final: 0.8207 (mtt) REVERT: D 326 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8334 (ttt) outliers start: 52 outliers final: 37 residues processed: 211 average time/residue: 0.1616 time to fit residues: 56.0712 Evaluate side-chains 200 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 112 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 300 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN B 371 HIS B 696 GLN B 710 ASN C 154 GLN C 367 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.071757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053044 restraints weight = 146849.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054390 restraints weight = 85087.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.055013 restraints weight = 60346.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055716 restraints weight = 50309.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.056024 restraints weight = 43387.028| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25190 Z= 0.181 Angle : 0.610 15.519 34202 Z= 0.305 Chirality : 0.044 0.274 3906 Planarity : 0.003 0.035 4296 Dihedral : 5.041 58.081 3710 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 2.39 % Allowed : 11.74 % Favored : 85.87 % 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 aren not related in a simple way. whole: -0.09 (0.16), residues: 3066 helix: 1.45 (0.15), residues: 1268 sheet: -0.60 (0.25), residues: 476 loop : -1.36 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 695 TYR 0.017 0.002 TYR B 232 PHE 0.044 0.002 PHE A 183 TRP 0.008 0.001 TRP C 167 HIS 0.015 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00404 (25154) covalent geometry : angle 0.60149 (34112) SS BOND : bond 0.00302 ( 18) SS BOND : angle 1.01091 ( 36) hydrogen bonds : bond 0.03240 ( 982) hydrogen bonds : angle 4.39872 ( 2892) link_NAG-ASN : bond 0.00533 ( 18) link_NAG-ASN : angle 2.54305 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.9107 (tpp) cc_final: 0.8808 (tpp) REVERT: A 200 MET cc_start: 0.7033 (tpp) cc_final: 0.6567 (tpp) REVERT: A 524 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6970 (p90) REVERT: A 789 GLU cc_start: 0.8243 (mp0) cc_final: 0.7941 (mp0) REVERT: A 817 MET cc_start: 0.5218 (mpp) cc_final: 0.4533 (mtm) REVERT: B 354 MET cc_start: 0.8171 (tpp) cc_final: 0.7356 (tpp) REVERT: C 200 MET cc_start: 0.6860 (tpp) cc_final: 0.6386 (tpp) REVERT: C 320 CYS cc_start: 0.4322 (OUTLIER) cc_final: 0.3884 (p) REVERT: C 637 PHE cc_start: 0.8651 (t80) cc_final: 0.8082 (m-80) REVERT: C 828 MET cc_start: 0.8512 (tpp) cc_final: 0.8181 (mtt) REVERT: D 326 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8397 (ttt) REVERT: D 354 MET cc_start: 0.8141 (tpp) cc_final: 0.7583 (tpp) REVERT: D 470 MET cc_start: 0.9048 (mpp) cc_final: 0.8841 (mpp) outliers start: 63 outliers final: 37 residues processed: 215 average time/residue: 0.1554 time to fit residues: 54.9572 Evaluate side-chains 194 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 533 PHE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 142 optimal weight: 3.9990 chunk 132 optimal weight: 0.0470 chunk 238 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 237 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.072526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053859 restraints weight = 145669.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055223 restraints weight = 83930.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.056139 restraints weight = 59356.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.056683 restraints weight = 47420.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.056973 restraints weight = 41164.919| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25190 Z= 0.117 Angle : 0.581 13.704 34202 Z= 0.286 Chirality : 0.043 0.277 3906 Planarity : 0.003 0.035 4296 Dihedral : 4.789 59.990 3708 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 1.82 % Allowed : 13.22 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 3066 helix: 1.39 (0.15), residues: 1268 sheet: -0.55 (0.25), residues: 474 loop : -1.34 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 377 TYR 0.020 0.001 TYR D 692 PHE 0.043 0.001 PHE C 183 TRP 0.008 0.001 TRP B 151 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00263 (25154) covalent geometry : angle 0.57246 (34112) SS BOND : bond 0.00260 ( 18) SS BOND : angle 0.91032 ( 36) hydrogen bonds : bond 0.02908 ( 982) hydrogen bonds : angle 4.33914 ( 2892) link_NAG-ASN : bond 0.00574 ( 18) link_NAG-ASN : angle 2.44972 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.001 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 112 MET cc_start: 0.9069 (tpp) cc_final: 0.8784 (tpp) REVERT: A 200 MET cc_start: 0.6849 (tpp) cc_final: 0.6349 (tpp) REVERT: A 524 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7188 (p90) REVERT: A 817 MET cc_start: 0.5248 (mpp) cc_final: 0.4501 (mtm) REVERT: B 354 MET cc_start: 0.8237 (tpp) cc_final: 0.7450 (tpp) REVERT: B 611 TRP cc_start: 0.5145 (m100) cc_final: 0.4854 (m100) REVERT: C 200 MET cc_start: 0.6737 (tpp) cc_final: 0.6235 (tpp) REVERT: C 320 CYS cc_start: 0.4198 (OUTLIER) cc_final: 0.3846 (p) REVERT: C 524 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7166 (p90) REVERT: C 637 PHE cc_start: 0.8638 (t80) cc_final: 0.8079 (m-80) REVERT: C 828 MET cc_start: 0.8512 (tpp) cc_final: 0.8192 (mtt) REVERT: D 326 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8401 (ttt) REVERT: D 354 MET cc_start: 0.8020 (tpp) cc_final: 0.7472 (tpp) outliers start: 48 outliers final: 37 residues processed: 204 average time/residue: 0.1681 time to fit residues: 55.8843 Evaluate side-chains 197 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 534 LYS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 2 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 116 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.071950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.053226 restraints weight = 146159.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.054566 restraints weight = 85033.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055444 restraints weight = 60130.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.055946 restraints weight = 48151.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056353 restraints weight = 42083.999| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25190 Z= 0.134 Angle : 0.596 14.002 34202 Z= 0.293 Chirality : 0.043 0.277 3906 Planarity : 0.003 0.036 4296 Dihedral : 4.794 59.789 3708 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 1.89 % Allowed : 13.14 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 3066 helix: 1.37 (0.15), residues: 1268 sheet: -0.65 (0.25), residues: 476 loop : -1.36 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 377 TYR 0.013 0.001 TYR B 232 PHE 0.042 0.001 PHE C 183 TRP 0.008 0.001 TRP B 151 HIS 0.007 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00301 (25154) covalent geometry : angle 0.58820 (34112) SS BOND : bond 0.00267 ( 18) SS BOND : angle 0.93713 ( 36) hydrogen bonds : bond 0.03031 ( 982) hydrogen bonds : angle 4.35925 ( 2892) link_NAG-ASN : bond 0.00552 ( 18) link_NAG-ASN : angle 2.42179 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 1.046 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 200 MET cc_start: 0.6889 (tpp) cc_final: 0.6429 (tpp) REVERT: A 524 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7101 (p90) REVERT: A 817 MET cc_start: 0.5340 (mpp) cc_final: 0.4581 (mtm) REVERT: B 354 MET cc_start: 0.8243 (tpp) cc_final: 0.7384 (tpp) REVERT: B 378 LYS cc_start: 0.7028 (tptp) cc_final: 0.6561 (tptp) REVERT: B 611 TRP cc_start: 0.5227 (m100) cc_final: 0.4956 (m100) REVERT: C 200 MET cc_start: 0.6807 (tpp) cc_final: 0.6310 (tpp) REVERT: C 320 CYS cc_start: 0.4161 (OUTLIER) cc_final: 0.3881 (p) REVERT: C 524 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6887 (p90) REVERT: C 637 PHE cc_start: 0.8642 (t80) cc_final: 0.8058 (m-80) REVERT: C 828 MET cc_start: 0.8620 (tpp) cc_final: 0.8341 (mtt) REVERT: D 326 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8426 (ttt) REVERT: D 354 MET cc_start: 0.8100 (tpp) cc_final: 0.7385 (tpp) REVERT: D 378 LYS cc_start: 0.6985 (tptp) cc_final: 0.6445 (tptp) REVERT: D 611 TRP cc_start: 0.5295 (m100) cc_final: 0.4943 (m100) outliers start: 50 outliers final: 38 residues processed: 200 average time/residue: 0.1630 time to fit residues: 53.4261 Evaluate side-chains 198 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 420 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 420 CYS Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 41 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 306 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 782 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.070873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052157 restraints weight = 146188.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053470 restraints weight = 85132.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054288 restraints weight = 60494.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054891 restraints weight = 48963.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.055241 restraints weight = 42150.152| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25190 Z= 0.169 Angle : 0.639 14.424 34202 Z= 0.316 Chirality : 0.044 0.275 3906 Planarity : 0.004 0.035 4296 Dihedral : 4.990 58.688 3708 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 1.89 % Allowed : 13.52 % Favored : 84.58 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 3066 helix: 1.28 (0.15), residues: 1266 sheet: -0.76 (0.25), residues: 476 loop : -1.42 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 392 TYR 0.017 0.001 TYR D 692 PHE 0.039 0.002 PHE C 183 TRP 0.010 0.001 TRP D 315 HIS 0.010 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00381 (25154) covalent geometry : angle 0.63134 (34112) SS BOND : bond 0.00315 ( 18) SS BOND : angle 0.99971 ( 36) hydrogen bonds : bond 0.03252 ( 982) hydrogen bonds : angle 4.47489 ( 2892) link_NAG-ASN : bond 0.00536 ( 18) link_NAG-ASN : angle 2.39995 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7040 (tpp) cc_final: 0.6590 (tpp) REVERT: A 524 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7488 (p90) REVERT: A 789 GLU cc_start: 0.8145 (mp0) cc_final: 0.7827 (mp0) REVERT: A 817 MET cc_start: 0.5264 (mpp) cc_final: 0.4443 (mtm) REVERT: B 354 MET cc_start: 0.8305 (tpp) cc_final: 0.7473 (tpp) REVERT: B 378 LYS cc_start: 0.6825 (tptp) cc_final: 0.6388 (tptp) REVERT: B 611 TRP cc_start: 0.5279 (m100) cc_final: 0.4972 (m100) REVERT: C 200 MET cc_start: 0.6956 (tpp) cc_final: 0.6470 (tpp) REVERT: C 524 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7332 (p90) REVERT: C 637 PHE cc_start: 0.8647 (t80) cc_final: 0.8057 (m-80) REVERT: C 666 SER cc_start: 0.8496 (m) cc_final: 0.8185 (t) REVERT: C 789 GLU cc_start: 0.8176 (mp0) cc_final: 0.7886 (mp0) REVERT: C 828 MET cc_start: 0.8614 (tpp) cc_final: 0.8329 (mtt) REVERT: D 326 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8431 (ttt) REVERT: D 354 MET cc_start: 0.8176 (tpp) cc_final: 0.7346 (tpp) REVERT: D 378 LYS cc_start: 0.7016 (tptp) cc_final: 0.6485 (tptp) REVERT: D 611 TRP cc_start: 0.5448 (m100) cc_final: 0.5093 (m100) REVERT: D 697 VAL cc_start: 0.8713 (m) cc_final: 0.8456 (p) outliers start: 50 outliers final: 37 residues processed: 202 average time/residue: 0.1554 time to fit residues: 51.8185 Evaluate side-chains 196 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 201 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 19 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.072074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053399 restraints weight = 145618.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.054744 restraints weight = 84466.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055660 restraints weight = 59507.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.056122 restraints weight = 47528.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.056524 restraints weight = 41424.271| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25190 Z= 0.110 Angle : 0.623 14.503 34202 Z= 0.303 Chirality : 0.043 0.280 3906 Planarity : 0.003 0.036 4296 Dihedral : 4.589 57.277 3705 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.23 % Rotamer: Outliers : 1.55 % Allowed : 13.98 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 3066 helix: 1.25 (0.15), residues: 1266 sheet: -0.69 (0.25), residues: 476 loop : -1.39 (0.18), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 694 TYR 0.020 0.001 TYR B 703 PHE 0.041 0.001 PHE C 183 TRP 0.009 0.001 TRP D 611 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00247 (25154) covalent geometry : angle 0.61561 (34112) SS BOND : bond 0.00264 ( 18) SS BOND : angle 1.12091 ( 36) hydrogen bonds : bond 0.03026 ( 982) hydrogen bonds : angle 4.40109 ( 2892) link_NAG-ASN : bond 0.00593 ( 18) link_NAG-ASN : angle 2.34303 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.6825 (tpp) cc_final: 0.6392 (tpp) REVERT: A 524 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7361 (p90) REVERT: A 705 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7331 (mmm) REVERT: A 817 MET cc_start: 0.5143 (mpp) cc_final: 0.4297 (mtm) REVERT: B 354 MET cc_start: 0.8307 (tpp) cc_final: 0.7443 (tpp) REVERT: B 378 LYS cc_start: 0.6793 (tptp) cc_final: 0.6369 (tptp) REVERT: B 611 TRP cc_start: 0.5379 (m100) cc_final: 0.5072 (m100) REVERT: C 200 MET cc_start: 0.6828 (tpp) cc_final: 0.6326 (tpp) REVERT: C 524 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7241 (p90) REVERT: C 637 PHE cc_start: 0.8647 (t80) cc_final: 0.8057 (m-80) REVERT: C 789 GLU cc_start: 0.8072 (mp0) cc_final: 0.7769 (mp0) REVERT: C 828 MET cc_start: 0.8621 (tpp) cc_final: 0.8331 (mtt) REVERT: D 326 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8392 (ttt) REVERT: D 354 MET cc_start: 0.8194 (tpp) cc_final: 0.7379 (tpp) REVERT: D 378 LYS cc_start: 0.6922 (tptp) cc_final: 0.6404 (tptp) REVERT: D 611 TRP cc_start: 0.5420 (m100) cc_final: 0.5088 (m100) REVERT: D 697 VAL cc_start: 0.8671 (m) cc_final: 0.8415 (p) outliers start: 41 outliers final: 33 residues processed: 194 average time/residue: 0.1585 time to fit residues: 50.5691 Evaluate side-chains 191 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 198 TRP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 PHE Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain C residue 198 TRP Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 524 PHE Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 793 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 248 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN B 782 ASN ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN D 782 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.068731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.049994 restraints weight = 147917.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051292 restraints weight = 86242.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052130 restraints weight = 61429.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052655 restraints weight = 49602.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052942 restraints weight = 43103.975| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25190 Z= 0.267 Angle : 0.766 14.509 34202 Z= 0.385 Chirality : 0.046 0.265 3906 Planarity : 0.004 0.048 4296 Dihedral : 5.419 52.444 3705 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.66 % Rotamer: Outliers : 1.86 % Allowed : 13.90 % Favored : 84.24 % 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 aren not related in a simple way. whole: -0.58 (0.16), residues: 3066 helix: 1.07 (0.15), residues: 1264 sheet: -1.05 (0.25), residues: 472 loop : -1.56 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 392 TYR 0.035 0.002 TYR D 692 PHE 0.059 0.003 PHE A 183 TRP 0.016 0.002 TRP D 315 HIS 0.014 0.002 HIS D 162 Details of bonding type rmsd covalent geometry : bond 0.00598 (25154) covalent geometry : angle 0.75959 (34112) SS BOND : bond 0.00430 ( 18) SS BOND : angle 1.18322 ( 36) hydrogen bonds : bond 0.04031 ( 982) hydrogen bonds : angle 4.82053 ( 2892) link_NAG-ASN : bond 0.00497 ( 18) link_NAG-ASN : angle 2.49676 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.83 seconds wall clock time: 77 minutes 46.79 seconds (4666.79 seconds total)