Starting phenix.real_space_refine on Sat Jul 4 15:53:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yff_33788/07_2026/7yff_33788.map" } resolution = 3.6 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= 0.009 sd= 0.073 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 106 5.16 5 C 13962 2.51 5 N 3713 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21820 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5605 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 733} Chain breaks: 6 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 19, 'PHE:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 13, 'GLN:plan1': 2, 'HIS:plan': 5, 'ASP:plan': 11, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 276 Chain: "B" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5193 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 33, 'TRANS': 706} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 16, 'ARG:plan': 28, 'HIS:plan': 5, 'ASP:plan': 14, 'TRP:plan': 2, 'GLN:plan1': 9, 'ASN:plan1': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 419 Chain: "C" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5605 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 33, 'TRANS': 733} Chain breaks: 6 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 583 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLU:plan': 19, 'PHE:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 13, 'GLN:plan1': 2, 'HIS:plan': 5, 'ASP:plan': 11, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 276 Chain: "D" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5193 Classifications: {'peptide': 740} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 33, 'TRANS': 706} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 630 Unresolved non-hydrogen angles: 799 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'TYR:plan': 7, 'GLU:plan': 16, 'ARG:plan': 28, 'HIS:plan': 5, 'ASP:plan': 14, 'TRP:plan': 2, 'GLN:plan1': 9, 'ASN:plan1': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 419 Chain: "E" 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: "F" 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: "G" 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: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'7RC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.80, per 1000 atoms: 0.22 Number of scatterers: 21820 At special positions: 0 Unit cell: (116.739, 138.159, 180.999, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 2 15.00 O 4037 8.00 N 3713 7.00 C 13962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 455 " - pdb=" SG CYS B 483 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 901 " - " ASN A 471 " " NAG A 902 " - " ASN A 276 " " NAG A 904 " - " ASN A 368 " " NAG C 901 " - " ASN C 471 " " NAG C 902 " - " ASN C 276 " " NAG C 903 " - " ASN C 61 " " NAG C 905 " - " ASN C 368 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 771 " " NAG G 1 " - " ASN C 771 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 821.9 milliseconds 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5616 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 32 sheets defined 45.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.733A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.721A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.572A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.796A pdb=" N ALA A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.554A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.811A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.653A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'A' and resid 626 through 658 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.578A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 removed outlier: 4.009A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS A 709 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.867A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 4.166A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 779 removed outlier: 3.669A pdb=" N SER A 775 " --> pdb=" O ASN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 811 through 840 removed outlier: 3.967A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.713A pdb=" N ALA B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.819A pdb=" N ILE B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 197 through 209 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 249 through 264 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 315 through 335 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.066A pdb=" N LEU B 578 " --> pdb=" O SER B 575 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 579 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 607 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.723A pdb=" N VAL B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 681 Processing helix chain 'B' and resid 717 through 726 Processing helix chain 'B' and resid 726 through 734 removed outlier: 3.582A pdb=" N TYR B 732 " --> pdb=" O ASP B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 748 removed outlier: 4.138A pdb=" N ALA B 744 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR B 746 " --> pdb=" O GLU B 743 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 747 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 770 removed outlier: 3.656A pdb=" N TYR B 765 " --> pdb=" O ALA B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 814 removed outlier: 3.578A pdb=" N GLY B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 813 " --> pdb=" O GLN B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 824 Processing helix chain 'B' and resid 841 through 869 removed outlier: 3.955A pdb=" N VAL B 869 " --> pdb=" O TRP B 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 53 Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.739A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.726A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.573A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.798A pdb=" N ALA C 284 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 357 through 360 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.558A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.815A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.651A pdb=" N SER C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 Processing helix chain 'C' and resid 626 through 658 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.579A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 710 removed outlier: 4.008A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.872A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.166A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 779 Processing helix chain 'C' and resid 784 through 793 Processing helix chain 'C' and resid 811 through 840 removed outlier: 4.011A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.718A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.818A pdb=" N ILE D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 249 through 264 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 487 through 500 Processing helix chain 'D' and resid 523 through 529 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.072A pdb=" N LEU D 578 " --> pdb=" O SER D 575 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 579 " --> pdb=" O ALA D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 607 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.723A pdb=" N VAL D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 681 Processing helix chain 'D' and resid 717 through 726 Processing helix chain 'D' and resid 726 through 734 removed outlier: 3.579A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 748 removed outlier: 4.156A pdb=" N ALA D 744 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR D 746 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 747 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 770 removed outlier: 3.655A pdb=" N TYR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 814 removed outlier: 3.562A pdb=" N GLY D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 813 " --> pdb=" O GLN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 824 Processing helix chain 'D' and resid 841 through 869 removed outlier: 3.956A pdb=" N VAL D 869 " --> pdb=" O TRP D 865 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.632A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 351 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.896A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 399 through 402 removed outlier: 5.776A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.565A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 490 removed outlier: 3.785A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N VAL A 490 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.923A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 117 through 118 removed outlier: 6.304A pdb=" N PHE B 117 " --> pdb=" O VAL B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 244 through 246 removed outlier: 6.564A pdb=" N ARG B 244 " --> pdb=" O PHE B 273 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 274 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 307 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 304 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 402 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER B 391 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 400 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 431 through 436 removed outlier: 4.062A pdb=" N THR B 436 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 447 Processing sheet with id=AB4, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AB5, first strand: chain 'B' and resid 557 through 559 removed outlier: 4.083A pdb=" N VAL B 557 " --> pdb=" O TYR B 789 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 755 through 759 removed outlier: 4.249A pdb=" N VAL B 563 " --> pdb=" O THR B 777 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 684 Processing sheet with id=AB8, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AB9, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.643A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 351 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 341 removed outlier: 3.897A pdb=" N ASP C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 402 removed outlier: 5.771A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.570A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 490 removed outlier: 3.789A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL C 490 " --> pdb=" O LYS C 495 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC6, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.983A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 117 through 118 removed outlier: 6.303A pdb=" N PHE D 117 " --> pdb=" O VAL D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 246 removed outlier: 6.564A pdb=" N ARG D 244 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 274 " --> pdb=" O PHE D 305 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 402 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER D 391 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL D 400 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 431 through 436 removed outlier: 4.057A pdb=" N THR D 436 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 443 through 447 Processing sheet with id=AD2, first strand: chain 'D' and resid 515 through 517 Processing sheet with id=AD3, first strand: chain 'D' and resid 557 through 559 removed outlier: 4.087A pdb=" N VAL D 557 " --> pdb=" O TYR D 789 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 755 through 759 removed outlier: 4.264A pdb=" N VAL D 563 " --> pdb=" O THR D 777 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 682 through 683 1052 hydrogen bonds defined for protein. 3051 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: 3.29 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.35: 7153 1.35 - 1.52: 7105 1.52 - 1.68: 7836 1.68 - 1.84: 176 1.84 - 2.00: 2 Bond restraints: 22272 Sorted by residual: bond pdb=" C07 7RC D 901 " pdb=" P01 7RC D 901 " ideal model delta sigma weight residual 1.853 2.003 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C07 7RC B 901 " pdb=" P01 7RC B 901 " ideal model delta sigma weight residual 1.853 2.002 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" CA VAL C 514 " pdb=" C VAL C 514 " ideal model delta sigma weight residual 1.523 1.432 0.091 1.27e-02 6.20e+03 5.17e+01 bond pdb=" C08 7RC B 901 " pdb=" O05 7RC B 901 " ideal model delta sigma weight residual 1.257 1.390 -0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" C08 7RC B 901 " pdb=" O01 7RC B 901 " ideal model delta sigma weight residual 1.256 1.389 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 30257 3.04 - 6.08: 121 6.08 - 9.13: 16 9.13 - 12.17: 3 12.17 - 15.21: 4 Bond angle restraints: 30401 Sorted by residual: angle pdb=" C GLU A 192 " pdb=" CA GLU A 192 " pdb=" CB GLU A 192 " ideal model delta sigma weight residual 117.23 107.19 10.04 1.36e+00 5.41e-01 5.45e+01 angle pdb=" C GLU D 815 " pdb=" N ILE D 816 " pdb=" CA ILE D 816 " ideal model delta sigma weight residual 120.46 113.12 7.34 1.37e+00 5.33e-01 2.87e+01 angle pdb=" C GLU B 815 " pdb=" N ILE B 816 " pdb=" CA ILE B 816 " ideal model delta sigma weight residual 120.46 113.13 7.33 1.37e+00 5.33e-01 2.86e+01 angle pdb=" C VAL C 514 " pdb=" CA VAL C 514 " pdb=" CB VAL C 514 " ideal model delta sigma weight residual 111.29 102.78 8.51 1.64e+00 3.72e-01 2.69e+01 angle pdb=" C06 7RC D 901 " pdb=" C07 7RC D 901 " pdb=" P01 7RC D 901 " ideal model delta sigma weight residual 116.22 101.01 15.21 3.00e+00 1.11e-01 2.57e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11544 17.92 - 35.84: 1287 35.84 - 53.76: 383 53.76 - 71.68: 45 71.68 - 89.60: 22 Dihedral angle restraints: 13281 sinusoidal: 4607 harmonic: 8674 Sorted by residual: dihedral pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " pdb=" SG CYS B 348 " pdb=" CB CYS B 348 " ideal model delta sinusoidal sigma weight residual 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS D 104 " pdb=" SG CYS D 104 " pdb=" SG CYS D 348 " pdb=" CB CYS D 348 " ideal model delta sinusoidal sigma weight residual 93.00 151.76 -58.76 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS B 773 " pdb=" SG CYS B 773 " pdb=" SG CYS B 828 " pdb=" CB CYS B 828 " ideal model delta sinusoidal sigma weight residual -86.00 -141.27 55.27 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 13278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 3616 0.246 - 0.493: 3 0.493 - 0.739: 0 0.739 - 0.986: 1 0.986 - 1.232: 1 Chirality restraints: 3621 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.17 -1.23 2.00e-01 2.50e+01 3.80e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.32e+01 ... (remaining 3618 not shown) Planarity restraints: 3881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.329 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG A 901 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.075 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 902 " 0.229 2.00e-02 2.50e+03 1.91e-01 4.54e+02 pdb=" C7 NAG A 902 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A 902 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG A 902 " -0.316 2.00e-02 2.50e+03 pdb=" O7 NAG A 902 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7RC B 901 " 0.102 2.00e-02 2.50e+03 2.08e-01 4.32e+02 pdb=" C08 7RC B 901 " -0.359 2.00e-02 2.50e+03 pdb=" O01 7RC B 901 " 0.132 2.00e-02 2.50e+03 pdb=" O05 7RC B 901 " 0.126 2.00e-02 2.50e+03 ... (remaining 3878 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 208 2.61 - 3.18: 20468 3.18 - 3.75: 32821 3.75 - 4.33: 41627 4.33 - 4.90: 70682 Nonbonded interactions: 165806 Sorted by model distance: nonbonded pdb=" OG1 THR D 541 " pdb=" O01 7RC D 901 " model vdw 2.036 3.040 nonbonded pdb=" OG1 THR B 541 " pdb=" O01 7RC B 901 " model vdw 2.045 3.040 nonbonded pdb=" N GLU D 558 " pdb=" OE1 GLU D 558 " model vdw 2.174 3.120 nonbonded pdb=" N GLU B 558 " pdb=" OE1 GLU B 558 " model vdw 2.174 3.120 nonbonded pdb=" O HIS A 780 " pdb=" N MET A 785 " model vdw 2.177 3.120 ... (remaining 165801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 38 through 902 or resid 904 through 905)) } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.310 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.730 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 : 0.004 0.150 22303 Z= 0.226 Angle : 0.557 15.209 30472 Z= 0.291 Chirality : 0.047 1.232 3621 Planarity : 0.008 0.287 3871 Dihedral : 16.559 89.597 7617 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Rotamer: Outliers : 0.30 % Allowed : 32.33 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2938 helix: 2.77 (0.16), residues: 1256 sheet: -1.29 (0.33), residues: 284 loop : -2.04 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 448 TYR 0.005 0.000 TYR A 647 PHE 0.009 0.001 PHE D 422 TRP 0.009 0.000 TRP A 768 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.23 (22272) covalent geometry : angle 0.54800 / 0.29 (30401) SS BOND : bond 0.00126 / 0.10 ( 16) SS BOND : angle 0.51984 / 0.42 ( 32) hydrogen bonds : bond 0.19285 / 13.28 ( 1052) hydrogen bonds : angle 6.73097 / 4.92 ( 3051) Misc. bond : bond 0.00052 / 0.03 ( 2) link_BETA1-4 : bond 0.00432 / 0.21 ( 3) link_BETA1-4 : angle 1.89482 / 1.43 ( 9) link_NAG-ASN : bond 0.01058 / 0.76 ( 10) link_NAG-ASN : angle 3.00646 / 2.21 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.766 Fit side-chains REVERT: D 830 ASN cc_start: 0.7436 (p0) cc_final: 0.7020 (p0) outliers start: 6 outliers final: 3 residues processed: 181 average time/residue: 0.1118 time to fit residues: 35.1299 Evaluate side-chains 174 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 521 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 764 ASN C 134 HIS C 521 ASN D 649 ASN D 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094853 restraints weight = 44845.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094002 restraints weight = 33644.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093408 restraints weight = 31477.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093858 restraints weight = 29823.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093893 restraints weight = 27611.691| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22303 Z= 0.165 Angle : 0.593 11.872 30472 Z= 0.302 Chirality : 0.043 0.382 3621 Planarity : 0.004 0.051 3871 Dihedral : 5.792 56.951 3483 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.48 % Favored : 91.35 % Rotamer: Outliers : 3.97 % Allowed : 28.46 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2938 helix: 2.10 (0.15), residues: 1264 sheet: -1.47 (0.30), residues: 332 loop : -2.10 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.018 0.001 TYR C 647 PHE 0.015 0.001 PHE A 810 TRP 0.008 0.001 TRP A 731 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (22272) covalent geometry : angle 0.58492 / 0.30 (30401) SS BOND : bond 0.00157 / 0.12 ( 16) SS BOND : angle 0.86662 / 0.69 ( 32) hydrogen bonds : bond 0.04909 / 3.42 ( 1052) hydrogen bonds : angle 5.37330 / 3.92 ( 3051) Misc. bond : bond 0.00056 / 0.03 ( 2) link_BETA1-4 : bond 0.00315 / 0.15 ( 3) link_BETA1-4 : angle 1.68424 / 1.30 ( 9) link_NAG-ASN : bond 0.00792 / 0.45 ( 10) link_NAG-ASN : angle 2.99092 / 2.03 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 163 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: A 702 MET cc_start: 0.8242 (mtt) cc_final: 0.8041 (mtt) REVERT: A 828 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8186 (tp) REVERT: B 544 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6708 (tt0) REVERT: B 773 CYS cc_start: 0.0476 (OUTLIER) cc_final: 0.0226 (t) REVERT: C 702 MET cc_start: 0.8257 (mtt) cc_final: 0.8054 (mtt) REVERT: C 828 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8243 (tp) REVERT: D 544 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: D 773 CYS cc_start: 0.0513 (OUTLIER) cc_final: 0.0234 (t) REVERT: D 830 ASN cc_start: 0.7989 (p0) cc_final: 0.7534 (p0) outliers start: 79 outliers final: 34 residues processed: 228 average time/residue: 0.1086 time to fit residues: 43.1676 Evaluate side-chains 205 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 627 PHE Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 10.0000 chunk 255 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 521 ASN A 812 ASN B 163 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS C 521 ASN C 780 HIS D 163 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.135796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093067 restraints weight = 44920.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092767 restraints weight = 32399.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092274 restraints weight = 28871.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092481 restraints weight = 29659.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092538 restraints weight = 26641.591| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22303 Z= 0.189 Angle : 0.582 9.692 30472 Z= 0.298 Chirality : 0.043 0.311 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.845 62.963 3481 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.34 % Favored : 91.42 % Rotamer: Outliers : 4.47 % Allowed : 29.12 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2938 helix: 1.80 (0.15), residues: 1270 sheet: -1.58 (0.29), residues: 336 loop : -2.20 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 532 TYR 0.015 0.001 TYR A 410 PHE 0.018 0.001 PHE A 810 TRP 0.007 0.001 TRP C 731 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (22272) covalent geometry : angle 0.57716 / 0.30 (30401) SS BOND : bond 0.00204 / 0.15 ( 16) SS BOND : angle 0.92256 / 0.74 ( 32) hydrogen bonds : bond 0.04383 / 3.06 ( 1052) hydrogen bonds : angle 5.09676 / 3.72 ( 3051) Misc. bond : bond 0.00008 / 0.00 ( 2) link_BETA1-4 : bond 0.00198 / 0.10 ( 3) link_BETA1-4 : angle 1.71714 / 1.31 ( 9) link_NAG-ASN : bond 0.00346 / 0.25 ( 10) link_NAG-ASN : angle 2.25661 / 1.59 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 172 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: A 392 TYR cc_start: 0.7168 (t80) cc_final: 0.6965 (t80) REVERT: A 828 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8245 (tp) REVERT: B 544 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: C 385 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: C 392 TYR cc_start: 0.7126 (t80) cc_final: 0.6924 (t80) REVERT: C 828 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8299 (tp) REVERT: D 544 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: D 830 ASN cc_start: 0.7956 (p0) cc_final: 0.7497 (p0) outliers start: 89 outliers final: 52 residues processed: 247 average time/residue: 0.1084 time to fit residues: 46.9155 Evaluate side-chains 222 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 100 optimal weight: 0.0000 chunk 205 optimal weight: 0.0270 chunk 96 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 216 optimal weight: 0.2980 chunk 246 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 overall best weight: 0.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 780 HIS ** D 649 ASN ** 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 = 0.4080 r_free = 0.4080 target = 0.138401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.095796 restraints weight = 44972.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096550 restraints weight = 31728.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095591 restraints weight = 25718.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095919 restraints weight = 27552.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096091 restraints weight = 24309.104| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22303 Z= 0.106 Angle : 0.539 9.618 30472 Z= 0.272 Chirality : 0.042 0.264 3621 Planarity : 0.004 0.055 3871 Dihedral : 5.596 70.093 3481 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.62 % Favored : 92.14 % Rotamer: Outliers : 3.87 % Allowed : 30.27 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2938 helix: 1.95 (0.15), residues: 1254 sheet: -1.83 (0.29), residues: 348 loop : -2.22 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 755 TYR 0.015 0.001 TYR A 647 PHE 0.015 0.001 PHE D 422 TRP 0.008 0.001 TRP B 662 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (22272) covalent geometry : angle 0.53455 / 0.27 (30401) SS BOND : bond 0.00191 / 0.15 ( 16) SS BOND : angle 0.81398 / 0.65 ( 32) hydrogen bonds : bond 0.03577 / 2.51 ( 1052) hydrogen bonds : angle 4.80167 / 3.50 ( 3051) Misc. bond : bond 0.00013 / 0.01 ( 2) link_BETA1-4 : bond 0.00181 / 0.09 ( 3) link_BETA1-4 : angle 1.82905 / 1.34 ( 9) link_NAG-ASN : bond 0.00385 / 0.28 ( 10) link_NAG-ASN : angle 2.06845 / 1.46 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 392 TYR cc_start: 0.7510 (t80) cc_final: 0.6863 (t80) REVERT: A 818 MET cc_start: 0.5271 (ptt) cc_final: 0.4790 (mmp) REVERT: A 828 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 170 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: B 544 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: B 773 CYS cc_start: 0.0645 (OUTLIER) cc_final: 0.0087 (t) REVERT: B 786 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 385 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: C 392 TYR cc_start: 0.7531 (t80) cc_final: 0.6864 (t80) REVERT: C 818 MET cc_start: 0.5142 (ptt) cc_final: 0.4640 (mmp) REVERT: C 828 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8138 (tp) REVERT: D 170 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: D 544 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: D 733 MET cc_start: 0.8161 (ttt) cc_final: 0.7953 (ttp) REVERT: D 773 CYS cc_start: 0.0582 (OUTLIER) cc_final: 0.0121 (t) REVERT: D 786 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8871 (t) REVERT: D 830 ASN cc_start: 0.7923 (p0) cc_final: 0.7530 (p0) outliers start: 77 outliers final: 38 residues processed: 241 average time/residue: 0.1174 time to fit residues: 49.3457 Evaluate side-chains 210 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 786 THR Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 39 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 780 HIS ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 ASN C 780 HIS C 812 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.135048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090209 restraints weight = 44726.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090312 restraints weight = 35532.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090306 restraints weight = 30121.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090314 restraints weight = 29937.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090428 restraints weight = 26593.806| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22303 Z= 0.236 Angle : 0.608 9.605 30472 Z= 0.309 Chirality : 0.044 0.300 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.806 69.031 3481 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.41 % Favored : 91.39 % Rotamer: Outliers : 4.92 % Allowed : 29.82 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.16), residues: 2938 helix: 1.71 (0.15), residues: 1276 sheet: -1.56 (0.30), residues: 318 loop : -2.34 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 532 TYR 0.016 0.001 TYR C 410 PHE 0.023 0.002 PHE C 533 TRP 0.007 0.001 TRP B 662 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (22272) covalent geometry : angle 0.60277 / 0.31 (30401) SS BOND : bond 0.00581 / 0.40 ( 16) SS BOND : angle 1.20647 / 0.95 ( 32) hydrogen bonds : bond 0.04112 / 2.87 ( 1052) hydrogen bonds : angle 4.88267 / 3.57 ( 3051) Misc. bond : bond 0.00006 / 0.00 ( 2) link_BETA1-4 : bond 0.00179 / 0.09 ( 3) link_BETA1-4 : angle 1.82412 / 1.40 ( 9) link_NAG-ASN : bond 0.00324 / 0.26 ( 10) link_NAG-ASN : angle 2.05491 / 1.52 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 163 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: A 392 TYR cc_start: 0.7358 (t80) cc_final: 0.6621 (t80) REVERT: A 828 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 544 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: C 385 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: C 392 TYR cc_start: 0.7521 (t80) cc_final: 0.6826 (t80) REVERT: C 828 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8226 (tp) REVERT: D 544 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: D 733 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8174 (ttp) REVERT: D 830 ASN cc_start: 0.8114 (p0) cc_final: 0.7722 (p0) REVERT: D 851 MET cc_start: 0.0981 (mmt) cc_final: 0.0778 (mmt) outliers start: 98 outliers final: 64 residues processed: 245 average time/residue: 0.1130 time to fit residues: 48.4198 Evaluate side-chains 231 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 160 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 208 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 283 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 282 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.137748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093144 restraints weight = 44580.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094229 restraints weight = 33061.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.094534 restraints weight = 24355.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094665 restraints weight = 23647.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.094746 restraints weight = 22335.125| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22303 Z= 0.109 Angle : 0.551 9.592 30472 Z= 0.275 Chirality : 0.042 0.258 3621 Planarity : 0.004 0.057 3871 Dihedral : 5.572 73.831 3481 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 3.92 % Allowed : 30.87 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.16), residues: 2938 helix: 1.97 (0.15), residues: 1238 sheet: -1.71 (0.29), residues: 328 loop : -2.18 (0.16), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.017 0.001 TYR A 647 PHE 0.015 0.001 PHE B 422 TRP 0.008 0.001 TRP A 247 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22272) covalent geometry : angle 0.54178 / 0.27 (30401) SS BOND : bond 0.00185 / 0.14 ( 16) SS BOND : angle 1.17453 / 0.88 ( 32) hydrogen bonds : bond 0.03422 / 2.42 ( 1052) hydrogen bonds : angle 4.69803 / 3.43 ( 3051) Misc. bond : bond 0.00016 / 0.01 ( 2) link_BETA1-4 : bond 0.00393 / 0.20 ( 3) link_BETA1-4 : angle 2.11705 / 1.58 ( 9) link_NAG-ASN : bond 0.00502 / 0.32 ( 10) link_NAG-ASN : angle 2.80798 / 1.96 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 168 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 385 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: A 392 TYR cc_start: 0.7246 (t80) cc_final: 0.6543 (t80) REVERT: A 818 MET cc_start: 0.5267 (ptt) cc_final: 0.4845 (mmp) REVERT: A 828 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 170 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: B 544 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6608 (tt0) REVERT: C 385 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: C 392 TYR cc_start: 0.7268 (t80) cc_final: 0.6542 (t80) REVERT: C 818 MET cc_start: 0.5157 (ptt) cc_final: 0.4684 (mmp) REVERT: C 828 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8196 (tp) REVERT: D 170 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: D 544 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: D 830 ASN cc_start: 0.8014 (p0) cc_final: 0.7619 (p0) outliers start: 78 outliers final: 55 residues processed: 234 average time/residue: 0.1164 time to fit residues: 46.8501 Evaluate side-chains 232 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 729 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 182 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091864 restraints weight = 44851.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093098 restraints weight = 33637.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092974 restraints weight = 27045.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093042 restraints weight = 27253.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093118 restraints weight = 25124.333| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22303 Z= 0.151 Angle : 0.562 9.580 30472 Z= 0.282 Chirality : 0.042 0.272 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.605 73.597 3481 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.20 % Favored : 91.59 % Rotamer: Outliers : 4.32 % Allowed : 30.37 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.16), residues: 2938 helix: 1.85 (0.15), residues: 1258 sheet: -1.70 (0.29), residues: 324 loop : -2.22 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.015 0.001 TYR A 647 PHE 0.014 0.001 PHE C 533 TRP 0.009 0.001 TRP B 662 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (22272) covalent geometry : angle 0.55534 / 0.28 (30401) SS BOND : bond 0.00245 / 0.18 ( 16) SS BOND : angle 1.19829 / 0.90 ( 32) hydrogen bonds : bond 0.03619 / 2.53 ( 1052) hydrogen bonds : angle 4.65688 / 3.40 ( 3051) Misc. bond : bond 0.00011 / 0.01 ( 2) link_BETA1-4 : bond 0.00262 / 0.14 ( 3) link_BETA1-4 : angle 1.85653 / 1.41 ( 9) link_NAG-ASN : bond 0.00271 / 0.19 ( 10) link_NAG-ASN : angle 2.43817 / 1.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 166 time to evaluate : 0.793 Fit side-chains REVERT: A 385 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: A 392 TYR cc_start: 0.7091 (t80) cc_final: 0.6495 (t80) REVERT: A 818 MET cc_start: 0.5282 (ptt) cc_final: 0.4871 (mmp) REVERT: A 828 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 170 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: B 544 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: C 385 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7997 (pm20) REVERT: C 392 TYR cc_start: 0.7114 (t80) cc_final: 0.6487 (t80) REVERT: C 818 MET cc_start: 0.5278 (ptt) cc_final: 0.4644 (mmp) REVERT: C 828 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8171 (tp) REVERT: D 170 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: D 544 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: D 668 ILE cc_start: 0.8795 (tp) cc_final: 0.8593 (tp) REVERT: D 830 ASN cc_start: 0.7981 (p0) cc_final: 0.7615 (p0) outliers start: 86 outliers final: 60 residues processed: 239 average time/residue: 0.1082 time to fit residues: 44.7889 Evaluate side-chains 234 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 99 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 491 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN D 649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.136804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093054 restraints weight = 44766.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093862 restraints weight = 33373.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093453 restraints weight = 26251.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093538 restraints weight = 27240.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093649 restraints weight = 24544.951| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22303 Z= 0.145 Angle : 0.568 9.567 30472 Z= 0.284 Chirality : 0.043 0.266 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.618 74.517 3481 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.51 % Favored : 91.29 % Rotamer: Outliers : 4.32 % Allowed : 30.67 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.16), residues: 2938 helix: 1.85 (0.15), residues: 1258 sheet: -1.86 (0.28), residues: 342 loop : -2.20 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.015 0.001 TYR A 647 PHE 0.015 0.001 PHE B 422 TRP 0.008 0.001 TRP D 662 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (22272) covalent geometry : angle 0.56233 / 0.28 (30401) SS BOND : bond 0.00496 / 0.34 ( 16) SS BOND : angle 1.17708 / 0.85 ( 32) hydrogen bonds : bond 0.03578 / 2.51 ( 1052) hydrogen bonds : angle 4.65236 / 3.39 ( 3051) Misc. bond : bond 0.00014 / 0.01 ( 2) link_BETA1-4 : bond 0.00238 / 0.12 ( 3) link_BETA1-4 : angle 1.83785 / 1.39 ( 9) link_NAG-ASN : bond 0.00263 / 0.19 ( 10) link_NAG-ASN : angle 2.30207 / 1.66 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 167 time to evaluate : 0.860 Fit side-chains REVERT: A 385 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 392 TYR cc_start: 0.6988 (t80) cc_final: 0.6427 (t80) REVERT: A 818 MET cc_start: 0.5264 (ptt) cc_final: 0.4861 (mmp) REVERT: A 828 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8110 (tp) REVERT: B 170 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8113 (mp10) REVERT: B 544 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: C 385 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: C 392 TYR cc_start: 0.7046 (t80) cc_final: 0.6441 (t80) REVERT: C 818 MET cc_start: 0.5256 (ptt) cc_final: 0.4636 (mmp) REVERT: C 828 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (tp) REVERT: D 170 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: D 544 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: D 830 ASN cc_start: 0.8224 (p0) cc_final: 0.7917 (p0) outliers start: 86 outliers final: 66 residues processed: 241 average time/residue: 0.1131 time to fit residues: 47.8937 Evaluate side-chains 243 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 39 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 649 ASN B 676 ASN ** D 676 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.133192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087483 restraints weight = 43508.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.089776 restraints weight = 26932.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091280 restraints weight = 20164.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.092271 restraints weight = 16860.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092765 restraints weight = 15075.372| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22303 Z= 0.184 Angle : 0.594 9.543 30472 Z= 0.299 Chirality : 0.043 0.276 3621 Planarity : 0.004 0.059 3871 Dihedral : 5.772 74.465 3481 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 4.42 % Allowed : 30.52 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2938 helix: 1.78 (0.15), residues: 1262 sheet: -1.88 (0.29), residues: 334 loop : -2.23 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.016 0.001 TYR A 647 PHE 0.019 0.002 PHE C 533 TRP 0.008 0.001 TRP D 662 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (22272) covalent geometry : angle 0.58764 / 0.30 (30401) SS BOND : bond 0.00211 / 0.16 ( 16) SS BOND : angle 1.52368 / 1.33 ( 32) hydrogen bonds : bond 0.03805 / 2.66 ( 1052) hydrogen bonds : angle 4.72768 / 3.45 ( 3051) Misc. bond : bond 0.00016 / 0.01 ( 2) link_BETA1-4 : bond 0.00220 / 0.12 ( 3) link_BETA1-4 : angle 1.80678 / 1.37 ( 9) link_NAG-ASN : bond 0.00275 / 0.21 ( 10) link_NAG-ASN : angle 2.27659 / 1.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 165 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 392 TYR cc_start: 0.6816 (t80) cc_final: 0.6410 (t80) REVERT: A 818 MET cc_start: 0.5363 (ptt) cc_final: 0.4980 (mmp) REVERT: A 828 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8228 (tp) REVERT: B 170 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: B 544 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: C 385 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: C 392 TYR cc_start: 0.6849 (t80) cc_final: 0.6312 (t80) REVERT: C 828 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8236 (tp) REVERT: D 170 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: D 544 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6725 (tt0) REVERT: D 830 ASN cc_start: 0.7994 (p0) cc_final: 0.7648 (p0) outliers start: 88 outliers final: 72 residues processed: 240 average time/residue: 0.1118 time to fit residues: 46.7450 Evaluate side-chains 243 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 164 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 184 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 152 optimal weight: 50.0000 chunk 190 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 228 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.136278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093879 restraints weight = 45197.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093998 restraints weight = 30347.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093751 restraints weight = 24943.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093740 restraints weight = 26638.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093761 restraints weight = 24352.638| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22303 Z= 0.152 Angle : 0.587 9.536 30472 Z= 0.293 Chirality : 0.043 0.262 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.728 75.536 3481 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.78 % Favored : 91.01 % Rotamer: Outliers : 4.22 % Allowed : 30.67 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.16), residues: 2938 helix: 1.78 (0.15), residues: 1262 sheet: -1.91 (0.29), residues: 334 loop : -2.24 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.016 0.001 TYR C 647 PHE 0.015 0.001 PHE D 422 TRP 0.009 0.001 TRP C 247 HIS 0.006 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (22272) covalent geometry : angle 0.57933 / 0.29 (30401) SS BOND : bond 0.00259 / 0.21 ( 16) SS BOND : angle 1.82287 / 1.46 ( 32) hydrogen bonds : bond 0.03659 / 2.56 ( 1052) hydrogen bonds : angle 4.69175 / 3.42 ( 3051) Misc. bond : bond 0.00017 / 0.01 ( 2) link_BETA1-4 : bond 0.00223 / 0.12 ( 3) link_BETA1-4 : angle 1.81303 / 1.36 ( 9) link_NAG-ASN : bond 0.00253 / 0.19 ( 10) link_NAG-ASN : angle 2.24031 / 1.65 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5876 Ramachandran restraints generated. 2938 Oldfield, 0 Emsley, 2938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 165 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 TYR cc_start: 0.6894 (t80) cc_final: 0.6286 (t80) REVERT: A 818 MET cc_start: 0.5676 (ptt) cc_final: 0.5138 (mmp) REVERT: A 828 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (tp) REVERT: B 170 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: B 544 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6666 (tt0) REVERT: C 326 MET cc_start: 0.8857 (mmt) cc_final: 0.8525 (mpp) REVERT: C 385 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7999 (pm20) REVERT: C 392 TYR cc_start: 0.6906 (t80) cc_final: 0.6245 (t80) REVERT: C 608 TRP cc_start: 0.8760 (m100) cc_final: 0.8545 (m100) REVERT: C 818 MET cc_start: 0.5231 (ptt) cc_final: 0.4727 (mmp) REVERT: C 828 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8225 (tp) REVERT: D 170 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: D 544 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: D 830 ASN cc_start: 0.8254 (p0) cc_final: 0.7923 (p0) outliers start: 84 outliers final: 71 residues processed: 237 average time/residue: 0.1161 time to fit residues: 47.9033 Evaluate side-chains 243 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 165 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 477 HIS Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 590 PHE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 280 HIS Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 436 CYS Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 786 GLU Chi-restraints excluded: chain C residue 828 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 422 PHE Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 687 VAL Chi-restraints excluded: chain D residue 718 THR Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 746 THR Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 815 GLU Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 243 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 260 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088616 restraints weight = 43434.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090920 restraints weight = 26693.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092428 restraints weight = 19958.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093473 restraints weight = 16649.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093925 restraints weight = 14856.596| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22303 Z= 0.145 Angle : 0.578 9.511 30472 Z= 0.288 Chirality : 0.042 0.256 3621 Planarity : 0.004 0.058 3871 Dihedral : 5.664 76.330 3481 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.95 % Favored : 90.84 % Rotamer: Outliers : 4.02 % Allowed : 30.62 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2938 helix: 1.85 (0.15), residues: 1258 sheet: -1.92 (0.29), residues: 334 loop : -2.25 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 755 TYR 0.014 0.001 TYR C 647 PHE 0.014 0.001 PHE B 422 TRP 0.009 0.001 TRP C 247 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (22272) covalent geometry : angle 0.57123 / 0.29 (30401) SS BOND : bond 0.00217 / 0.16 ( 16) SS BOND : angle 1.66960 / 1.35 ( 32) hydrogen bonds : bond 0.03524 / 2.47 ( 1052) hydrogen bonds : angle 4.62375 / 3.37 ( 3051) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-4 : bond 0.00184 / 0.10 ( 3) link_BETA1-4 : angle 1.78115 / 1.34 ( 9) link_NAG-ASN : bond 0.00250 / 0.18 ( 10) link_NAG-ASN : angle 2.20467 / 1.63 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.45 seconds wall clock time: 59 minutes 42.11 seconds (3582.11 seconds total)