Starting phenix.real_space_refine on Sat Jul 4 08:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmw_54069/07_2026/9rmw_54069.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 134 5.16 5 Cl 4 4.86 5 C 12442 2.51 5 N 2998 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 18965 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3165 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 3208 Chain: "E" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1491 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1381 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1491 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3165 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 3187 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 3208 Chain: "H" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1381 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 3} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Unusual residues: {'CYZ': 1, 'PLM': 4} Inner-chain residues flagged as termini: ['pdbres="GLU B1004 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 87 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'CYZ': 1, 'PLM': 3} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 4} Inner-chain residues flagged as termini: ['pdbres="GLU D1006 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.49, per 1000 atoms: 0.29 Number of scatterers: 18965 At special positions: 0 Unit cell: (123.333, 113.265, 145.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 4 17.00 S 134 16.00 O 3386 8.00 N 2998 7.00 C 12442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 611 " - pdb=" SG CYS D 611 " distance=2.11 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 611 " - pdb=" SG CYS C 611 " distance=1.96 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 725.6 milliseconds 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 26 sheets defined 57.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 445 through 459 removed outlier: 3.716A pdb=" N ASP A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 491 removed outlier: 3.907A pdb=" N VAL A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.698A pdb=" N GLU A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 568 Processing helix chain 'A' and resid 594 through 608 removed outlier: 4.115A pdb=" N LEU A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 647 removed outlier: 3.812A pdb=" N ALA A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 663 removed outlier: 3.688A pdb=" N LEU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 686 through 698 removed outlier: 3.787A pdb=" N LYS A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 719 removed outlier: 3.549A pdb=" N LYS A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 732 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.755A pdb=" N VAL A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 846 removed outlier: 4.335A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 removed outlier: 3.556A pdb=" N MET B 436 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE B 437 " --> pdb=" O HIS B 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 433 through 437' Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 445 through 459 removed outlier: 4.464A pdb=" N LYS B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.725A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 544 through 568 Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 617 through 641 removed outlier: 4.529A pdb=" N ASN B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 647 Processing helix chain 'B' and resid 657 through 664 removed outlier: 4.218A pdb=" N LEU B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 686 through 698 removed outlier: 3.673A pdb=" N TRP B 693 " --> pdb=" O TYR B 689 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 removed outlier: 3.653A pdb=" N GLY B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 713 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 716 " --> pdb=" O VAL B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.540A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 777 removed outlier: 3.536A pdb=" N LEU B 770 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 777 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 removed outlier: 3.703A pdb=" N LYS B 783 " --> pdb=" O GLY B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 846 removed outlier: 3.650A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 removed outlier: 3.538A pdb=" N LEU E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.697A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 217 removed outlier: 3.520A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 129 removed outlier: 3.626A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 162 Processing helix chain 'F' and resid 177 through 212 removed outlier: 3.556A pdb=" N LEU F 208 " --> pdb=" O ARG F 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 209 " --> pdb=" O HIS F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 30 removed outlier: 3.538A pdb=" N LEU G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.698A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 217 removed outlier: 3.521A pdb=" N ILE G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.716A pdb=" N ASP C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA C 451 " --> pdb=" O CYS C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 491 removed outlier: 3.907A pdb=" N VAL C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.698A pdb=" N GLU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 568 Processing helix chain 'C' and resid 594 through 608 removed outlier: 4.114A pdb=" N LEU C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 647 removed outlier: 3.811A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 663 removed outlier: 3.689A pdb=" N LEU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 686 through 698 removed outlier: 3.787A pdb=" N LYS C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 698 " --> pdb=" O THR C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 719 removed outlier: 3.549A pdb=" N LYS C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 732 Processing helix chain 'C' and resid 765 through 778 removed outlier: 3.755A pdb=" N VAL C 772 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU C 773 " --> pdb=" O ASN C 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 774 " --> pdb=" O LEU C 770 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 777 " --> pdb=" O LEU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 788 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 846 removed outlier: 4.336A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 437 removed outlier: 3.555A pdb=" N MET D 436 " --> pdb=" O ASN D 433 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE D 437 " --> pdb=" O HIS D 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 433 through 437' Processing helix chain 'D' and resid 438 through 441 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.465A pdb=" N LYS D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 removed outlier: 3.727A pdb=" N LEU D 489 " --> pdb=" O MET D 485 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 544 through 568 Processing helix chain 'D' and resid 594 through 607 Processing helix chain 'D' and resid 617 through 641 removed outlier: 4.531A pdb=" N ASN D 641 " --> pdb=" O SER D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 647 Processing helix chain 'D' and resid 657 through 664 removed outlier: 4.219A pdb=" N LEU D 661 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 683 Processing helix chain 'D' and resid 686 through 698 removed outlier: 3.673A pdb=" N TRP D 693 " --> pdb=" O TYR D 689 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 698 " --> pdb=" O THR D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 removed outlier: 3.654A pdb=" N GLY D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 716 " --> pdb=" O VAL D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 737 removed outlier: 3.539A pdb=" N GLN D 736 " --> pdb=" O GLU D 732 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 737 " --> pdb=" O TYR D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 777 removed outlier: 3.536A pdb=" N LEU D 770 " --> pdb=" O THR D 766 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 777 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 789 removed outlier: 3.703A pdb=" N LYS D 783 " --> pdb=" O GLY D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 813 Processing helix chain 'D' and resid 814 through 846 removed outlier: 3.650A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 30 Processing helix chain 'H' and resid 92 through 105 Processing helix chain 'H' and resid 105 through 129 removed outlier: 3.626A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 162 Processing helix chain 'H' and resid 177 through 212 removed outlier: 3.556A pdb=" N LEU H 208 " --> pdb=" O ARG H 204 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 209 " --> pdb=" O HIS H 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421 removed outlier: 5.844A pdb=" N VAL A 419 " --> pdb=" O ALA A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.666A pdb=" N GLU A 444 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 474 through 475 Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.826A pdb=" N ALA A 757 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 519 through 520 removed outlier: 3.765A pdb=" N LYS A 752 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.564A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET A 743 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 520 removed outlier: 4.028A pdb=" N LYS B 752 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 669 through 671 removed outlier: 6.831A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 61 Processing sheet with id=AB2, first strand: chain 'E' and resid 65 through 67 Processing sheet with id=AB3, first strand: chain 'F' and resid 59 through 61 Processing sheet with id=AB4, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AB5, first strand: chain 'G' and resid 57 through 61 Processing sheet with id=AB6, first strand: chain 'G' and resid 65 through 67 Processing sheet with id=AB7, first strand: chain 'C' and resid 418 through 421 removed outlier: 5.845A pdb=" N VAL C 419 " --> pdb=" O ALA C 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 429 through 430 removed outlier: 3.666A pdb=" N GLU C 444 " --> pdb=" O MET C 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 474 through 475 Processing sheet with id=AC1, first strand: chain 'C' and resid 497 through 498 removed outlier: 3.825A pdb=" N ALA C 757 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 519 through 520 removed outlier: 3.765A pdb=" N LYS C 752 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 668 through 671 removed outlier: 6.564A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 743 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AC5, first strand: chain 'D' and resid 519 through 520 removed outlier: 4.029A pdb=" N LYS D 752 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 669 through 671 removed outlier: 6.831A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 61 Processing sheet with id=AC8, first strand: chain 'H' and resid 65 through 67 1014 hydrogen bonds defined for protein. 2950 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: 3.09 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3208 1.33 - 1.45: 5170 1.45 - 1.57: 10766 1.57 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19372 Sorted by residual: bond pdb=" N CYS B 837 " pdb=" CA CYS B 837 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.38e+00 bond pdb=" N CYS D 837 " pdb=" CA CYS D 837 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.37e+00 bond pdb=" N CYS A 837 " pdb=" CA CYS A 837 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.32e+00 bond pdb=" N CYS C 837 " pdb=" CA CYS C 837 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.22e+00 bond pdb=" C1 PLM D1001 " pdb=" O2 PLM D1001 " ideal model delta sigma weight residual 1.249 1.206 0.043 2.00e-02 2.50e+03 4.64e+00 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 25540 1.56 - 3.12: 457 3.12 - 4.68: 84 4.68 - 6.24: 23 6.24 - 7.80: 8 Bond angle restraints: 26112 Sorted by residual: angle pdb=" C ALA A 757 " pdb=" N THR A 758 " pdb=" CA THR A 758 " ideal model delta sigma weight residual 121.80 129.04 -7.24 2.44e+00 1.68e-01 8.80e+00 angle pdb=" C ALA C 757 " pdb=" N THR C 758 " pdb=" CA THR C 758 " ideal model delta sigma weight residual 121.80 128.98 -7.18 2.44e+00 1.68e-01 8.66e+00 angle pdb=" CA CYS C 611 " pdb=" CB CYS C 611 " pdb=" SG CYS C 611 " ideal model delta sigma weight residual 114.40 120.62 -6.22 2.30e+00 1.89e-01 7.31e+00 angle pdb=" CA CYS A 611 " pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " ideal model delta sigma weight residual 114.40 120.60 -6.20 2.30e+00 1.89e-01 7.26e+00 angle pdb=" C PRO B 468 " pdb=" N ASP B 469 " pdb=" CA ASP B 469 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.92e+00 ... (remaining 26107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 11213 27.95 - 55.89: 216 55.89 - 83.84: 47 83.84 - 111.79: 7 111.79 - 139.74: 17 Dihedral angle restraints: 11500 sinusoidal: 4616 harmonic: 6884 Sorted by residual: dihedral pdb=" CB CYS B 611 " pdb=" SG CYS B 611 " pdb=" SG CYS C 611 " pdb=" CB CYS C 611 " ideal model delta sinusoidal sigma weight residual 93.00 153.67 -60.67 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS A 611 " pdb=" SG CYS A 611 " pdb=" SG CYS D 611 " pdb=" CB CYS D 611 " ideal model delta sinusoidal sigma weight residual 93.00 152.14 -59.14 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA SER B 425 " pdb=" C SER B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta harmonic sigma weight residual 0.00 25.68 -25.68 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 11497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2488 0.057 - 0.114: 368 0.114 - 0.172: 32 0.172 - 0.229: 7 0.229 - 0.286: 7 Chirality restraints: 2902 Sorted by residual: chirality pdb=" C8 CYZ A1004 " pdb=" C1 CYZ A1004 " pdb=" N1 CYZ A1004 " pdb=" N2 CYZ A1004 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C8 CYZ C1004 " pdb=" C1 CYZ C1004 " pdb=" N1 CYZ C1004 " pdb=" N2 CYZ C1004 " both_signs ideal model delta sigma weight residual False 2.20 2.48 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1 CYZ C1004 " pdb=" C2 CYZ C1004 " pdb=" C6 CYZ C1004 " pdb=" C8 CYZ C1004 " both_signs ideal model delta sigma weight residual False 2.79 2.52 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2899 not shown) Planarity restraints: 3178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 714 " 0.256 9.50e-02 1.11e+02 1.15e-01 9.95e+00 pdb=" NE ARG C 714 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 714 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 714 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 714 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 714 " -0.256 9.50e-02 1.11e+02 1.15e-01 9.91e+00 pdb=" NE ARG A 714 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 714 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 714 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 714 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 716 " 0.239 9.50e-02 1.11e+02 1.08e-01 9.39e+00 pdb=" NE ARG C 716 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 716 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 716 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 716 " -0.000 2.00e-02 2.50e+03 ... (remaining 3175 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1900 2.75 - 3.29: 18660 3.29 - 3.82: 30038 3.82 - 4.36: 36758 4.36 - 4.90: 63498 Nonbonded interactions: 150854 Sorted by model distance: nonbonded pdb=" OE2 GLU B 508 " pdb=" ND2 ASN C 769 " model vdw 2.211 3.120 nonbonded pdb=" OE1 GLU C 727 " pdb=" OH TYR C 754 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU A 727 " pdb=" OH TYR A 754 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLU B 727 " pdb=" OH TYR B 754 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLU D 727 " pdb=" OH TYR D 754 " model vdw 2.274 3.040 ... (remaining 150849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 417 through 426 or resid 428 through 573 or resid 591 thro \ ugh 648 or (resid 649 through 650 and (name N or name CA or name C or name O or \ name CB )) or resid 651 through 729 or resid 731 through 732 or resid 734 throug \ h 1001)) selection = (chain 'B' and (resid 417 through 426 or resid 428 through 729 or resid 731 thro \ ugh 732 or resid 734 through 736 or (resid 737 and (name N or name CA or name C \ or name O or name CB )) or resid 738 through 796 or resid 805 through 845 or (re \ sid 846 and (name N or name CA or name C or name O or name CB )) or resid 1001)) \ selection = (chain 'C' and (resid 417 through 426 or resid 428 through 573 or resid 591 thro \ ugh 648 or (resid 649 through 650 and (name N or name CA or name C or name O or \ name CB )) or resid 651 through 729 or resid 731 through 732 or resid 734 throug \ h 1001)) selection = (chain 'D' and (resid 417 through 426 or resid 428 through 729 or resid 731 thro \ ugh 732 or resid 734 through 736 or (resid 737 and (name N or name CA or name C \ or name O or name CB )) or resid 738 through 796 or resid 805 through 845 or (re \ sid 846 and (name N or name CA or name C or name O or name CB )) or resid 1001)) \ } ncs_group { reference = (chain 'E' and (resid 7 through 40 or resid 58 through 73 or (resid 74 and (name \ N or name CA or name C or name O or name CB )) or resid 75 through 84 or (resid \ 85 through 92 and (name N or name CA or name C or name O or name CB )) or resid \ 93 through 128 or (resid 129 and (name N or name CA or name C or name O or name \ CB )) or resid 130 through 214 or resid 401)) selection = (chain 'F' and (resid 7 through 85 or resid 91 through 162 or resid 172 through \ 401)) selection = (chain 'G' and (resid 7 through 40 or resid 58 through 73 or (resid 74 and (name \ N or name CA or name C or name O or name CB )) or resid 75 through 84 or (resid \ 85 through 92 and (name N or name CA or name C or name O or name CB )) or resid \ 93 through 128 or (resid 129 and (name N or name CA or name C or name O or name \ CB )) or resid 130 through 214 or resid 401)) selection = (chain 'H' and (resid 7 through 85 or resid 91 through 162 or resid 172 through \ 401)) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.840 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 0.074 19390 Z= 0.171 Angle : 0.554 7.798 26140 Z= 0.281 Chirality : 0.042 0.286 2902 Planarity : 0.007 0.115 3178 Dihedral : 12.967 139.737 7058 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -0.95 (0.18), residues: 2340 helix: 0.95 (0.16), residues: 1290 sheet: -2.27 (0.70), residues: 50 loop : -2.83 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG C 716 TYR 0.009 0.001 TYR C 462 PHE 0.009 0.001 PHE F 141 TRP 0.013 0.001 TRP B 693 HIS 0.003 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (19372) covalent geometry : angle 0.55157 / 0.28 (26112) SS BOND : bond 0.02792 / 1.28 ( 14) SS BOND : angle 1.74955 / 0.89 ( 28) hydrogen bonds : bond 0.25017 / 16.47 ( 1014) hydrogen bonds : angle 7.04546 / 4.96 ( 2950) Misc. bond : bond 0.00526 / 0.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.6986 (m-80) cc_final: 0.6775 (m-80) REVERT: A 449 ASP cc_start: 0.6957 (m-30) cc_final: 0.6582 (m-30) REVERT: A 692 MET cc_start: 0.7967 (mtp) cc_final: 0.7578 (mpp) REVERT: B 495 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6760 (mp0) REVERT: B 506 VAL cc_start: 0.8780 (m) cc_final: 0.8556 (p) REVERT: B 693 TRP cc_start: 0.7623 (t-100) cc_final: 0.7400 (t-100) REVERT: B 694 THR cc_start: 0.8013 (m) cc_final: 0.7757 (p) REVERT: B 732 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6617 (tp30) REVERT: B 736 GLN cc_start: 0.7166 (mt0) cc_final: 0.6787 (mt0) REVERT: F 18 PHE cc_start: 0.8209 (t80) cc_final: 0.7907 (t80) REVERT: F 22 SER cc_start: 0.8031 (m) cc_final: 0.7808 (m) REVERT: C 471 LYS cc_start: 0.7168 (mttt) cc_final: 0.6258 (mtpt) REVERT: C 513 PHE cc_start: 0.6648 (m-80) cc_final: 0.6090 (m-80) REVERT: C 525 MET cc_start: 0.7460 (ttp) cc_final: 0.7237 (ttm) REVERT: C 526 ILE cc_start: 0.8149 (pt) cc_final: 0.7721 (tp) REVERT: C 748 ASN cc_start: 0.8030 (m-40) cc_final: 0.7759 (m-40) REVERT: D 429 MET cc_start: 0.6949 (mtm) cc_final: 0.6745 (mtp) REVERT: D 441 ASP cc_start: 0.7574 (m-30) cc_final: 0.6931 (p0) REVERT: D 453 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 485 MET cc_start: 0.6766 (ttm) cc_final: 0.6313 (ptm) REVERT: B 1004 GLU cc_start: 0.5379 (tt0) cc_final: 0.5129 (tt0) REVERT: C 1006 GLU cc_start: 0.6406 (mm-30) cc_final: 0.5439 (mm-30) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.6414 time to fit residues: 357.6639 Evaluate side-chains 291 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN A 608 GLN B 641 ASN E 79 GLN C 597 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN D 609 GLN D 736 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.202884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127208 restraints weight = 50907.637| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.11 r_work: 0.3246 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19390 Z= 0.150 Angle : 0.604 9.771 26140 Z= 0.312 Chirality : 0.041 0.172 2902 Planarity : 0.004 0.078 3178 Dihedral : 9.433 97.626 2984 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.70 % Allowed : 13.69 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.25 (0.18), residues: 2340 helix: 1.86 (0.15), residues: 1320 sheet: -2.32 (0.61), residues: 48 loop : -2.24 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 37 TYR 0.021 0.002 TYR D 754 PHE 0.012 0.001 PHE H 107 TRP 0.011 0.001 TRP D 693 HIS 0.007 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (19372) covalent geometry : angle 0.60050 / 0.31 (26112) SS BOND : bond 0.00216 / 0.13 ( 14) SS BOND : angle 1.98215 / 1.58 ( 28) hydrogen bonds : bond 0.04985 / 3.25 ( 1014) hydrogen bonds : angle 4.21964 / 2.95 ( 2950) Misc. bond : bond 0.00028 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 325 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.6668 (m-80) cc_final: 0.6075 (m-80) REVERT: A 436 MET cc_start: 0.7895 (pmt) cc_final: 0.7677 (pmm) REVERT: A 571 TYR cc_start: 0.8646 (m-80) cc_final: 0.8398 (m-80) REVERT: A 679 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 692 MET cc_start: 0.7816 (mtp) cc_final: 0.7245 (mpp) REVERT: A 841 ARG cc_start: 0.6370 (mmt180) cc_final: 0.5916 (mmt180) REVERT: B 424 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: B 428 VAL cc_start: 0.6675 (t) cc_final: 0.6175 (p) REVERT: B 449 ASP cc_start: 0.5850 (p0) cc_final: 0.5172 (p0) REVERT: B 453 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8024 (mp0) REVERT: B 476 ASP cc_start: 0.6121 (m-30) cc_final: 0.5318 (p0) REVERT: B 495 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6907 (mp0) REVERT: B 518 MET cc_start: 0.6205 (ttm) cc_final: 0.5928 (ptm) REVERT: B 549 MET cc_start: 0.7706 (ttm) cc_final: 0.7404 (ttm) REVERT: B 693 TRP cc_start: 0.7925 (t-100) cc_final: 0.7574 (t-100) REVERT: B 719 LYS cc_start: 0.8585 (mttm) cc_final: 0.8271 (mtmm) REVERT: B 732 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6234 (tp30) REVERT: B 736 GLN cc_start: 0.6618 (mt0) cc_final: 0.6306 (mt0) REVERT: B 782 ASP cc_start: 0.6409 (m-30) cc_final: 0.6141 (m-30) REVERT: B 794 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.4867 (mp0) REVERT: E 37 ARG cc_start: 0.7230 (mmm-85) cc_final: 0.6926 (mmm-85) REVERT: E 117 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6639 (mtp) REVERT: F 22 SER cc_start: 0.7734 (m) cc_final: 0.7489 (m) REVERT: F 131 ARG cc_start: 0.7218 (mmt180) cc_final: 0.6172 (tmt170) REVERT: G 106 ILE cc_start: 0.7896 (tt) cc_final: 0.7512 (tp) REVERT: G 129 LYS cc_start: 0.8523 (mttm) cc_final: 0.8133 (mtmm) REVERT: G 131 ARG cc_start: 0.5963 (tpt170) cc_final: 0.4310 (mtt180) REVERT: C 679 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 692 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7230 (mpp) REVERT: C 696 MET cc_start: 0.7592 (mtm) cc_final: 0.7275 (mtm) REVERT: C 748 ASN cc_start: 0.8300 (m-40) cc_final: 0.7965 (m-40) REVERT: C 810 SER cc_start: 0.8466 (m) cc_final: 0.8131 (t) REVERT: C 845 LYS cc_start: 0.5925 (tttt) cc_final: 0.5603 (ptpt) REVERT: D 429 MET cc_start: 0.6976 (mtm) cc_final: 0.6713 (mtp) REVERT: D 436 MET cc_start: 0.7204 (ptt) cc_final: 0.6825 (ttp) REVERT: D 441 ASP cc_start: 0.7713 (m-30) cc_final: 0.6809 (p0) REVERT: D 442 LYS cc_start: 0.6285 (mttt) cc_final: 0.5986 (mtpp) REVERT: D 485 MET cc_start: 0.6447 (ttm) cc_final: 0.6169 (ptm) REVERT: D 719 LYS cc_start: 0.8358 (mttm) cc_final: 0.7615 (tttm) REVERT: D 721 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7739 (mmmm) outliers start: 52 outliers final: 15 residues processed: 354 average time/residue: 0.5690 time to fit residues: 227.2660 Evaluate side-chains 283 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 50 optimal weight: 4.9990 chunk 147 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 0.0000 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 813 ASN F 132 HIS C 434 HIS D 608 GLN D 736 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.201557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.123546 restraints weight = 54981.180| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.68 r_work: 0.3243 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19390 Z= 0.125 Angle : 0.533 8.912 26140 Z= 0.275 Chirality : 0.040 0.209 2902 Planarity : 0.004 0.068 3178 Dihedral : 8.167 80.664 2984 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.96 % Allowed : 16.08 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.79 (0.18), residues: 2340 helix: 2.23 (0.15), residues: 1322 sheet: -2.33 (0.59), residues: 48 loop : -1.89 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 765 TYR 0.012 0.001 TYR C 695 PHE 0.016 0.001 PHE B 568 TRP 0.019 0.001 TRP D 693 HIS 0.003 0.001 HIS H 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (19372) covalent geometry : angle 0.53015 / 0.27 (26112) SS BOND : bond 0.00367 / 0.13 ( 14) SS BOND : angle 1.79584 / 1.41 ( 28) hydrogen bonds : bond 0.04421 / 2.87 ( 1014) hydrogen bonds : angle 3.79923 / 2.66 ( 2950) Misc. bond : bond 0.00025 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7814 (mtp) cc_final: 0.7341 (mpp) REVERT: A 744 LYS cc_start: 0.7162 (tttm) cc_final: 0.6890 (ttmt) REVERT: A 756 VAL cc_start: 0.6940 (t) cc_final: 0.6702 (m) REVERT: B 424 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: B 495 GLU cc_start: 0.7709 (mt-10) cc_final: 0.6970 (mp0) REVERT: B 518 MET cc_start: 0.6428 (ttm) cc_final: 0.6086 (ptm) REVERT: B 549 MET cc_start: 0.8097 (ttm) cc_final: 0.7816 (ttm) REVERT: B 693 TRP cc_start: 0.7942 (t-100) cc_final: 0.7576 (t-100) REVERT: B 719 LYS cc_start: 0.8577 (mttm) cc_final: 0.8250 (mtmm) REVERT: B 737 ARG cc_start: 0.6224 (mmt90) cc_final: 0.5570 (ptm160) REVERT: B 738 LYS cc_start: 0.8387 (pmtt) cc_final: 0.7638 (ttpt) REVERT: B 794 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.4949 (mp0) REVERT: E 37 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7096 (mmm-85) REVERT: E 117 MET cc_start: 0.7165 (mtp) cc_final: 0.6852 (mtp) REVERT: E 126 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7604 (tm-30) REVERT: F 22 SER cc_start: 0.7729 (m) cc_final: 0.7514 (p) REVERT: F 65 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7147 (ptp90) REVERT: G 24 MET cc_start: 0.7675 (tpt) cc_final: 0.7110 (tpt) REVERT: G 106 ILE cc_start: 0.8240 (tt) cc_final: 0.7880 (tp) REVERT: G 126 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7232 (pp20) REVERT: G 129 LYS cc_start: 0.8571 (mttm) cc_final: 0.8230 (mtmm) REVERT: G 131 ARG cc_start: 0.6271 (tpt170) cc_final: 0.6033 (mmp-170) REVERT: G 211 THR cc_start: 0.6193 (m) cc_final: 0.5964 (p) REVERT: C 482 TRP cc_start: 0.5302 (m100) cc_final: 0.4970 (m100) REVERT: C 679 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: C 692 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (mpp) REVERT: C 748 ASN cc_start: 0.8478 (m-40) cc_final: 0.8118 (m-40) REVERT: C 810 SER cc_start: 0.8611 (m) cc_final: 0.8286 (t) REVERT: C 845 LYS cc_start: 0.6188 (tttt) cc_final: 0.5870 (ptpt) REVERT: D 436 MET cc_start: 0.7183 (ptt) cc_final: 0.6802 (ttp) REVERT: D 441 ASP cc_start: 0.7772 (m-30) cc_final: 0.6894 (p0) REVERT: D 442 LYS cc_start: 0.6336 (mttt) cc_final: 0.6028 (mtpp) REVERT: D 485 MET cc_start: 0.6356 (ttm) cc_final: 0.6031 (ptm) REVERT: D 522 ILE cc_start: 0.7208 (mp) cc_final: 0.6887 (mp) REVERT: D 719 LYS cc_start: 0.8379 (mttm) cc_final: 0.7690 (tttm) REVERT: D 721 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7819 (mmmm) outliers start: 57 outliers final: 22 residues processed: 341 average time/residue: 0.5590 time to fit residues: 214.8333 Evaluate side-chains 292 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 845 LYS Chi-restraints excluded: chain B residue 424 GLU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 50.0000 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 232 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 ASN A 731 ASN B 608 GLN B 731 ASN F 132 HIS F 160 ASN C 434 HIS ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN D 736 GLN H 132 HIS H 160 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.197496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120793 restraints weight = 58761.624| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.74 r_work: 0.3212 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19390 Z= 0.155 Angle : 0.552 13.266 26140 Z= 0.285 Chirality : 0.041 0.237 2902 Planarity : 0.004 0.058 3178 Dihedral : 7.748 69.805 2984 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.96 % Allowed : 17.74 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.82 (0.18), residues: 2340 helix: 2.06 (0.15), residues: 1338 sheet: -2.08 (0.55), residues: 78 loop : -1.58 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.022 0.001 TYR C 695 PHE 0.014 0.001 PHE F 201 TRP 0.020 0.001 TRP D 693 HIS 0.004 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (19372) covalent geometry : angle 0.54959 / 0.28 (26112) SS BOND : bond 0.00442 / 0.30 ( 14) SS BOND : angle 1.67646 / 1.28 ( 28) hydrogen bonds : bond 0.04588 / 2.98 ( 1014) hydrogen bonds : angle 3.80710 / 2.66 ( 2950) Misc. bond : bond 0.00048 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7838 (mtp) cc_final: 0.7352 (mpp) REVERT: B 495 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7074 (mp0) REVERT: B 518 MET cc_start: 0.7009 (ttm) cc_final: 0.6473 (ptm) REVERT: B 549 MET cc_start: 0.8380 (ttm) cc_final: 0.8114 (ttm) REVERT: B 693 TRP cc_start: 0.8025 (t-100) cc_final: 0.7707 (t-100) REVERT: B 710 GLU cc_start: 0.7349 (tt0) cc_final: 0.7026 (tt0) REVERT: B 712 VAL cc_start: 0.8255 (t) cc_final: 0.8045 (p) REVERT: B 719 LYS cc_start: 0.8637 (mttm) cc_final: 0.8332 (mtmm) REVERT: B 737 ARG cc_start: 0.6463 (mmt90) cc_final: 0.5560 (ptm160) REVERT: B 738 LYS cc_start: 0.8574 (pmtt) cc_final: 0.7913 (ttpt) REVERT: E 37 ARG cc_start: 0.7664 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: E 126 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7570 (tm-30) REVERT: E 206 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7547 (mtpt) REVERT: F 22 SER cc_start: 0.7882 (m) cc_final: 0.7664 (p) REVERT: F 37 ARG cc_start: 0.5444 (OUTLIER) cc_final: 0.4873 (mtt-85) REVERT: G 24 MET cc_start: 0.7897 (tpt) cc_final: 0.7174 (tpt) REVERT: G 95 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7064 (tt0) REVERT: G 126 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7475 (tm-30) REVERT: G 129 LYS cc_start: 0.8763 (mttm) cc_final: 0.8475 (mtmt) REVERT: G 204 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7077 (mtt90) REVERT: C 482 TRP cc_start: 0.5761 (m100) cc_final: 0.5523 (m100) REVERT: C 679 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 692 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7329 (mpp) REVERT: C 748 ASN cc_start: 0.8530 (m-40) cc_final: 0.8187 (m-40) REVERT: C 810 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8415 (t) REVERT: C 845 LYS cc_start: 0.6001 (tttt) cc_final: 0.5456 (ttpp) REVERT: D 436 MET cc_start: 0.7137 (ptt) cc_final: 0.6705 (ttp) REVERT: D 441 ASP cc_start: 0.7850 (m-30) cc_final: 0.7415 (t0) REVERT: D 592 GLU cc_start: 0.8054 (tp30) cc_final: 0.7670 (tt0) REVERT: D 693 TRP cc_start: 0.7816 (t60) cc_final: 0.7285 (t-100) REVERT: D 719 LYS cc_start: 0.8524 (mttm) cc_final: 0.7965 (ttpp) REVERT: H 200 MET cc_start: 0.8486 (mtp) cc_final: 0.8203 (mtm) REVERT: C 1006 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5700 (mm-30) REVERT: D 1006 GLU cc_start: 0.6203 (mt-10) cc_final: 0.5911 (mt-10) outliers start: 57 outliers final: 24 residues processed: 317 average time/residue: 0.5564 time to fit residues: 198.4966 Evaluate side-chains 282 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 480 LYS Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 120 optimal weight: 0.0980 chunk 194 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN B 731 ASN F 132 HIS F 160 ASN C 434 HIS C 731 ASN D 608 GLN H 132 HIS H 160 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.199276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122870 restraints weight = 56061.872| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.67 r_work: 0.3237 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19390 Z= 0.118 Angle : 0.505 9.097 26140 Z= 0.262 Chirality : 0.040 0.210 2902 Planarity : 0.003 0.048 3178 Dihedral : 6.745 65.225 2984 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 3.01 % Allowed : 18.52 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2340 helix: 2.26 (0.15), residues: 1338 sheet: -1.70 (0.58), residues: 68 loop : -1.46 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 37 TYR 0.013 0.001 TYR D 669 PHE 0.011 0.001 PHE A 630 TRP 0.016 0.001 TRP D 693 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (19372) covalent geometry : angle 0.50367 / 0.26 (26112) SS BOND : bond 0.00313 / 0.12 ( 14) SS BOND : angle 1.24930 / 0.92 ( 28) hydrogen bonds : bond 0.04034 / 2.62 ( 1014) hydrogen bonds : angle 3.63705 / 2.54 ( 2950) Misc. bond : bond 0.00028 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 280 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7798 (mtp) cc_final: 0.7297 (mpp) REVERT: B 423 MET cc_start: 0.7706 (mmm) cc_final: 0.7395 (tpt) REVERT: B 495 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7116 (mp0) REVERT: B 518 MET cc_start: 0.7176 (ttm) cc_final: 0.6614 (ptm) REVERT: B 549 MET cc_start: 0.8308 (ttm) cc_final: 0.8050 (ttm) REVERT: B 592 GLU cc_start: 0.7945 (pm20) cc_final: 0.7553 (tp30) REVERT: B 693 TRP cc_start: 0.7998 (t-100) cc_final: 0.7704 (t-100) REVERT: B 719 LYS cc_start: 0.8598 (mttm) cc_final: 0.8302 (mtmm) REVERT: B 737 ARG cc_start: 0.6456 (mmt90) cc_final: 0.5579 (ptm160) REVERT: B 738 LYS cc_start: 0.8579 (pmtt) cc_final: 0.7958 (ttpt) REVERT: E 37 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7368 (mmm-85) REVERT: E 126 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7650 (tm-30) REVERT: E 206 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7536 (mtpt) REVERT: F 22 SER cc_start: 0.7802 (m) cc_final: 0.7565 (p) REVERT: F 37 ARG cc_start: 0.5507 (OUTLIER) cc_final: 0.4897 (mtt-85) REVERT: F 65 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7457 (ptp90) REVERT: G 12 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (tt) REVERT: G 24 MET cc_start: 0.7859 (tpt) cc_final: 0.7343 (tpt) REVERT: G 95 GLU cc_start: 0.7741 (mm-30) cc_final: 0.6989 (tt0) REVERT: G 126 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7609 (tm-30) REVERT: G 129 LYS cc_start: 0.8757 (mttm) cc_final: 0.8465 (mtmt) REVERT: G 204 ARG cc_start: 0.7420 (mtt180) cc_final: 0.7083 (mtt90) REVERT: C 482 TRP cc_start: 0.5735 (m100) cc_final: 0.5478 (m100) REVERT: C 509 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6954 (pp20) REVERT: C 692 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7293 (mpp) REVERT: C 738 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7029 (pmtt) REVERT: C 743 MET cc_start: 0.6929 (ppp) cc_final: 0.6628 (ppp) REVERT: C 748 ASN cc_start: 0.8516 (m-40) cc_final: 0.8168 (m-40) REVERT: C 810 SER cc_start: 0.8685 (m) cc_final: 0.8400 (t) REVERT: D 436 MET cc_start: 0.7224 (ptt) cc_final: 0.6832 (ttp) REVERT: D 441 ASP cc_start: 0.7883 (m-30) cc_final: 0.7439 (t0) REVERT: D 669 TYR cc_start: 0.6921 (p90) cc_final: 0.6661 (p90) REVERT: D 693 TRP cc_start: 0.7836 (t60) cc_final: 0.7375 (t-100) REVERT: D 719 LYS cc_start: 0.8542 (mttm) cc_final: 0.7880 (tttm) REVERT: H 31 ASP cc_start: 0.8425 (p0) cc_final: 0.7785 (p0) REVERT: H 200 MET cc_start: 0.8507 (mtp) cc_final: 0.8237 (mtm) REVERT: H 203 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7451 (t0) REVERT: C 1006 GLU cc_start: 0.6011 (mm-30) cc_final: 0.5677 (mm-30) outliers start: 58 outliers final: 25 residues processed: 308 average time/residue: 0.5654 time to fit residues: 196.5465 Evaluate side-chains 284 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 686 ILE Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 70 optimal weight: 0.0270 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 0.1980 chunk 219 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN B 731 ASN F 132 HIS F 160 ASN C 434 HIS D 608 GLN H 132 HIS H 160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122285 restraints weight = 55710.109| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.66 r_work: 0.3238 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19390 Z= 0.122 Angle : 0.517 11.772 26140 Z= 0.265 Chirality : 0.040 0.173 2902 Planarity : 0.003 0.043 3178 Dihedral : 6.384 59.298 2984 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 3.58 % Allowed : 18.46 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2340 helix: 2.34 (0.14), residues: 1336 sheet: -1.91 (0.49), residues: 98 loop : -1.28 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 37 TYR 0.017 0.001 TYR A 695 PHE 0.011 0.001 PHE A 630 TRP 0.015 0.001 TRP D 693 HIS 0.003 0.001 HIS G 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (19372) covalent geometry : angle 0.51464 / 0.26 (26112) SS BOND : bond 0.00334 / 0.21 ( 14) SS BOND : angle 1.68828 / 1.26 ( 28) hydrogen bonds : bond 0.04053 / 2.63 ( 1014) hydrogen bonds : angle 3.61644 / 2.52 ( 2950) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7886 (mtp) cc_final: 0.7293 (mpp) REVERT: A 743 MET cc_start: 0.7293 (ppp) cc_final: 0.7038 (ppp) REVERT: B 495 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7129 (mp0) REVERT: B 518 MET cc_start: 0.7170 (ttm) cc_final: 0.6602 (ptm) REVERT: B 592 GLU cc_start: 0.7936 (pm20) cc_final: 0.7531 (tp30) REVERT: B 693 TRP cc_start: 0.8026 (t-100) cc_final: 0.7676 (t-100) REVERT: B 710 GLU cc_start: 0.7496 (tt0) cc_final: 0.7135 (tt0) REVERT: B 719 LYS cc_start: 0.8643 (mttm) cc_final: 0.8264 (mtmm) REVERT: B 737 ARG cc_start: 0.6460 (mmt90) cc_final: 0.5586 (ptm160) REVERT: B 738 LYS cc_start: 0.8595 (pmtt) cc_final: 0.7976 (ttpt) REVERT: E 37 ARG cc_start: 0.7653 (mmm-85) cc_final: 0.7003 (mmm-85) REVERT: E 95 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6725 (pt0) REVERT: E 126 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7656 (tm-30) REVERT: E 206 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7510 (mtpt) REVERT: F 22 SER cc_start: 0.7838 (m) cc_final: 0.7631 (m) REVERT: F 37 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.4952 (mtt-85) REVERT: F 65 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7375 (ptp90) REVERT: G 12 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7674 (tt) REVERT: G 24 MET cc_start: 0.7884 (tpt) cc_final: 0.7353 (tpt) REVERT: G 95 GLU cc_start: 0.7739 (mm-30) cc_final: 0.6969 (tt0) REVERT: G 126 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7764 (tm-30) REVERT: G 129 LYS cc_start: 0.8747 (mttm) cc_final: 0.8451 (mtmt) REVERT: G 204 ARG cc_start: 0.7362 (mtt180) cc_final: 0.6948 (mtt90) REVERT: C 478 ASP cc_start: 0.7638 (m-30) cc_final: 0.6716 (t0) REVERT: C 509 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6943 (pp20) REVERT: C 592 GLU cc_start: 0.8330 (pm20) cc_final: 0.7525 (mm-30) REVERT: C 692 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7346 (mpp) REVERT: C 738 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7059 (pmtt) REVERT: C 743 MET cc_start: 0.6960 (ppp) cc_final: 0.6446 (ppp) REVERT: C 748 ASN cc_start: 0.8518 (m-40) cc_final: 0.8184 (m-40) REVERT: C 810 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8376 (t) REVERT: D 436 MET cc_start: 0.7175 (ptt) cc_final: 0.6873 (ttp) REVERT: D 441 ASP cc_start: 0.7918 (m-30) cc_final: 0.6901 (p0) REVERT: D 693 TRP cc_start: 0.7836 (t60) cc_final: 0.7470 (t-100) REVERT: D 696 MET cc_start: 0.7286 (mtt) cc_final: 0.6934 (mtt) REVERT: D 719 LYS cc_start: 0.8545 (mttm) cc_final: 0.7889 (tttm) REVERT: H 31 ASP cc_start: 0.8452 (p0) cc_final: 0.7873 (p0) REVERT: C 1006 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5638 (mm-30) outliers start: 69 outliers final: 26 residues processed: 312 average time/residue: 0.5605 time to fit residues: 197.1936 Evaluate side-chains 291 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 728 SER Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 480 LYS Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 213 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 160 ASN C 434 HIS D 608 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.199726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123886 restraints weight = 61937.820| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.31 r_work: 0.3163 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19390 Z= 0.158 Angle : 0.553 11.294 26140 Z= 0.284 Chirality : 0.042 0.344 2902 Planarity : 0.004 0.043 3178 Dihedral : 6.780 59.049 2984 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 19.40 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2340 helix: 2.22 (0.14), residues: 1336 sheet: -1.96 (0.46), residues: 106 loop : -1.28 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 507 TYR 0.014 0.001 TYR C 545 PHE 0.015 0.001 PHE F 201 TRP 0.014 0.001 TRP D 693 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (19372) covalent geometry : angle 0.55151 / 0.28 (26112) SS BOND : bond 0.00365 / 0.25 ( 14) SS BOND : angle 1.29255 / 0.95 ( 28) hydrogen bonds : bond 0.04496 / 2.92 ( 1014) hydrogen bonds : angle 3.72833 / 2.61 ( 2950) Misc. bond : bond 0.00044 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7710 (mtp) cc_final: 0.7164 (mpp) REVERT: A 743 MET cc_start: 0.6931 (ppp) cc_final: 0.6580 (ppp) REVERT: B 495 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7121 (mp0) REVERT: B 592 GLU cc_start: 0.7818 (pm20) cc_final: 0.7222 (tp30) REVERT: B 693 TRP cc_start: 0.7909 (t-100) cc_final: 0.7558 (t-100) REVERT: B 710 GLU cc_start: 0.7526 (tt0) cc_final: 0.7132 (tt0) REVERT: B 719 LYS cc_start: 0.8564 (mttm) cc_final: 0.8159 (mtmm) REVERT: B 737 ARG cc_start: 0.6152 (mmt90) cc_final: 0.5300 (ptm160) REVERT: B 738 LYS cc_start: 0.8554 (pmtt) cc_final: 0.7920 (ttpt) REVERT: E 37 ARG cc_start: 0.7338 (mmm-85) cc_final: 0.6694 (mmm-85) REVERT: E 95 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6514 (pt0) REVERT: E 126 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7548 (tm-30) REVERT: E 206 LYS cc_start: 0.7242 (mtpt) cc_final: 0.6973 (mtpt) REVERT: F 22 SER cc_start: 0.7119 (m) cc_final: 0.6908 (m) REVERT: F 37 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4641 (mtt-85) REVERT: G 12 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7060 (tt) REVERT: G 24 MET cc_start: 0.7214 (tpt) cc_final: 0.6622 (tpt) REVERT: G 95 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6737 (tt0) REVERT: G 126 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7637 (tm-30) REVERT: G 129 LYS cc_start: 0.8496 (mttm) cc_final: 0.8208 (mtmt) REVERT: G 204 ARG cc_start: 0.6824 (mtt180) cc_final: 0.6443 (mtt90) REVERT: C 478 ASP cc_start: 0.7669 (m-30) cc_final: 0.6898 (t0) REVERT: C 509 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6935 (pp20) REVERT: C 592 GLU cc_start: 0.8193 (pm20) cc_final: 0.7979 (pm20) REVERT: C 692 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7126 (mpp) REVERT: C 730 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6352 (mpp) REVERT: C 738 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6876 (pmtt) REVERT: C 748 ASN cc_start: 0.8359 (m-40) cc_final: 0.7981 (m-40) REVERT: C 810 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 436 MET cc_start: 0.7226 (ptt) cc_final: 0.7022 (ttp) REVERT: D 441 ASP cc_start: 0.7844 (m-30) cc_final: 0.7317 (t0) REVERT: D 683 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7738 (mtm180) REVERT: D 693 TRP cc_start: 0.7801 (t60) cc_final: 0.7570 (t-100) REVERT: D 719 LYS cc_start: 0.8553 (mttm) cc_final: 0.7785 (tttm) REVERT: H 31 ASP cc_start: 0.8050 (p0) cc_final: 0.7390 (p0) REVERT: C 1006 GLU cc_start: 0.5704 (mm-30) cc_final: 0.5350 (mm-30) outliers start: 63 outliers final: 30 residues processed: 312 average time/residue: 0.5738 time to fit residues: 201.1470 Evaluate side-chains 297 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 214 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 134 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 91 optimal weight: 0.0970 chunk 184 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN B 731 ASN F 132 HIS F 160 ASN C 434 HIS ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN H 132 HIS H 160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127330 restraints weight = 59038.328| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.36 r_work: 0.3240 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19390 Z= 0.112 Angle : 0.511 11.349 26140 Z= 0.262 Chirality : 0.040 0.346 2902 Planarity : 0.003 0.043 3178 Dihedral : 6.170 56.511 2984 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.43 % Rotamer: Outliers : 2.44 % Allowed : 20.90 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2340 helix: 2.52 (0.14), residues: 1322 sheet: -1.78 (0.46), residues: 108 loop : -1.24 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 37 TYR 0.019 0.001 TYR A 695 PHE 0.011 0.001 PHE A 630 TRP 0.015 0.001 TRP D 693 HIS 0.003 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (19372) covalent geometry : angle 0.50996 / 0.26 (26112) SS BOND : bond 0.00400 / 0.27 ( 14) SS BOND : angle 1.07014 / 0.78 ( 28) hydrogen bonds : bond 0.03878 / 2.52 ( 1014) hydrogen bonds : angle 3.60947 / 2.52 ( 2950) Misc. bond : bond 0.00020 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: A 692 MET cc_start: 0.7761 (mtp) cc_final: 0.7262 (mpp) REVERT: A 743 MET cc_start: 0.7109 (ppp) cc_final: 0.6615 (ppp) REVERT: B 495 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7118 (mp0) REVERT: B 592 GLU cc_start: 0.7767 (pm20) cc_final: 0.7268 (tp30) REVERT: B 693 TRP cc_start: 0.7937 (t-100) cc_final: 0.7638 (t-100) REVERT: B 710 GLU cc_start: 0.7540 (tt0) cc_final: 0.7161 (tt0) REVERT: B 719 LYS cc_start: 0.8568 (mttm) cc_final: 0.8166 (mtmm) REVERT: B 737 ARG cc_start: 0.6173 (mmt90) cc_final: 0.5339 (ptm160) REVERT: B 738 LYS cc_start: 0.8591 (pmtt) cc_final: 0.7974 (ttpt) REVERT: E 37 ARG cc_start: 0.7429 (mmm-85) cc_final: 0.6786 (mmm-85) REVERT: E 95 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6529 (pt0) REVERT: E 126 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7606 (tm-30) REVERT: E 204 ARG cc_start: 0.6934 (mtt-85) cc_final: 0.6513 (mtt90) REVERT: E 206 LYS cc_start: 0.7296 (mtpt) cc_final: 0.6994 (mtpt) REVERT: F 22 SER cc_start: 0.7301 (m) cc_final: 0.7087 (m) REVERT: F 39 VAL cc_start: 0.7461 (p) cc_final: 0.7215 (t) REVERT: F 65 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6876 (ptp90) REVERT: G 12 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7203 (tt) REVERT: G 24 MET cc_start: 0.7411 (tpt) cc_final: 0.6921 (tpt) REVERT: G 95 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6811 (tt0) REVERT: G 106 ILE cc_start: 0.8076 (tt) cc_final: 0.7695 (tp) REVERT: G 126 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7676 (tm-30) REVERT: G 129 LYS cc_start: 0.8568 (mttm) cc_final: 0.8275 (mtmt) REVERT: G 204 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6599 (mtt90) REVERT: C 478 ASP cc_start: 0.7369 (m-30) cc_final: 0.6688 (t0) REVERT: C 509 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: C 692 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7167 (mpp) REVERT: C 730 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6371 (mpp) REVERT: C 738 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6933 (pmtt) REVERT: C 743 MET cc_start: 0.6941 (ppp) cc_final: 0.6237 (ppp) REVERT: C 748 ASN cc_start: 0.8344 (m-40) cc_final: 0.7992 (m-40) REVERT: C 810 SER cc_start: 0.8310 (OUTLIER) cc_final: 0.7988 (t) REVERT: D 441 ASP cc_start: 0.7842 (m-30) cc_final: 0.6769 (p0) REVERT: D 683 ARG cc_start: 0.8413 (mmm160) cc_final: 0.7769 (mtm180) REVERT: D 705 THR cc_start: 0.8152 (p) cc_final: 0.7940 (p) REVERT: D 719 LYS cc_start: 0.8564 (mttm) cc_final: 0.7866 (ttpp) REVERT: H 22 SER cc_start: 0.7277 (OUTLIER) cc_final: 0.6907 (m) REVERT: H 31 ASP cc_start: 0.8231 (p0) cc_final: 0.7543 (p0) REVERT: A 1006 GLU cc_start: 0.5209 (mt-10) cc_final: 0.5000 (mm-30) REVERT: C 1006 GLU cc_start: 0.5698 (mm-30) cc_final: 0.5389 (mm-30) outliers start: 47 outliers final: 20 residues processed: 311 average time/residue: 0.5799 time to fit residues: 203.7872 Evaluate side-chains 298 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 692 MET Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 738 LYS Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 148 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 121 optimal weight: 50.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 608 GLN B 731 ASN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 160 ASN C 434 HIS ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN H 160 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.195485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118737 restraints weight = 56036.427| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.12 r_work: 0.3177 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 19390 Z= 0.257 Angle : 0.644 11.154 26140 Z= 0.328 Chirality : 0.045 0.329 2902 Planarity : 0.004 0.043 3178 Dihedral : 8.014 58.498 2984 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 2.75 % Allowed : 21.52 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.89 (0.18), residues: 2340 helix: 2.01 (0.14), residues: 1314 sheet: -2.03 (0.40), residues: 146 loop : -1.18 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 507 TYR 0.021 0.002 TYR C 545 PHE 0.020 0.002 PHE F 201 TRP 0.013 0.002 TRP B 482 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.26 (19372) covalent geometry : angle 0.64288 / 0.33 (26112) SS BOND : bond 0.00423 / 0.30 ( 14) SS BOND : angle 1.47554 / 1.08 ( 28) hydrogen bonds : bond 0.05275 / 3.44 ( 1014) hydrogen bonds : angle 3.95716 / 2.76 ( 2950) Misc. bond : bond 0.00083 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 MET cc_start: 0.7736 (mtp) cc_final: 0.7190 (mpp) REVERT: A 743 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6556 (ppp) REVERT: A 748 ASN cc_start: 0.8100 (m-40) cc_final: 0.7748 (m-40) REVERT: B 495 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7160 (mp0) REVERT: B 693 TRP cc_start: 0.8009 (t-100) cc_final: 0.7742 (t-100) REVERT: B 710 GLU cc_start: 0.7505 (tt0) cc_final: 0.7109 (tt0) REVERT: B 719 LYS cc_start: 0.8629 (mttm) cc_final: 0.8225 (mtmm) REVERT: B 737 ARG cc_start: 0.6272 (mmt90) cc_final: 0.5285 (ptm160) REVERT: B 738 LYS cc_start: 0.8621 (pmtt) cc_final: 0.7966 (ttpt) REVERT: E 37 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.6803 (mmm-85) REVERT: E 95 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6356 (pt0) REVERT: E 126 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7629 (tm-30) REVERT: E 204 ARG cc_start: 0.7074 (mtt-85) cc_final: 0.6525 (mtt90) REVERT: F 22 SER cc_start: 0.7371 (m) cc_final: 0.7145 (m) REVERT: F 37 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.4740 (mtt-85) REVERT: F 39 VAL cc_start: 0.7360 (p) cc_final: 0.7146 (t) REVERT: F 65 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.6827 (ptp90) REVERT: G 12 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7209 (tt) REVERT: G 24 MET cc_start: 0.7402 (tpt) cc_final: 0.6888 (tpt) REVERT: G 95 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6727 (tt0) REVERT: G 126 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7680 (tm-30) REVERT: G 129 LYS cc_start: 0.8582 (mttm) cc_final: 0.8295 (mtmt) REVERT: C 478 ASP cc_start: 0.7593 (m-30) cc_final: 0.6971 (t0) REVERT: C 509 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6989 (pp20) REVERT: C 592 GLU cc_start: 0.8278 (pm20) cc_final: 0.7629 (mm-30) REVERT: C 730 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6360 (mpp) REVERT: C 748 ASN cc_start: 0.8306 (m-40) cc_final: 0.7958 (m-40) REVERT: C 810 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8061 (t) REVERT: D 441 ASP cc_start: 0.7959 (m-30) cc_final: 0.7428 (t0) REVERT: D 592 GLU cc_start: 0.7871 (tp30) cc_final: 0.7488 (tt0) REVERT: D 660 ASP cc_start: 0.6730 (m-30) cc_final: 0.6395 (m-30) REVERT: D 683 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7799 (mtm180) REVERT: D 705 THR cc_start: 0.7986 (p) cc_final: 0.7640 (p) REVERT: D 710 GLU cc_start: 0.7525 (tt0) cc_final: 0.7324 (tt0) REVERT: D 719 LYS cc_start: 0.8589 (mttm) cc_final: 0.7866 (tttm) REVERT: C 1006 GLU cc_start: 0.5841 (mm-30) cc_final: 0.5417 (mm-30) REVERT: D 1006 GLU cc_start: 0.5331 (OUTLIER) cc_final: 0.4172 (mt-10) outliers start: 53 outliers final: 25 residues processed: 308 average time/residue: 0.5558 time to fit residues: 193.2596 Evaluate side-chains 294 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 519 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 0.5980 chunk 147 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN B 731 ASN F 132 HIS F 160 ASN C 434 HIS ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN D 608 GLN H 132 HIS H 160 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.200823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125072 restraints weight = 58319.490| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.07 r_work: 0.3242 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19390 Z= 0.115 Angle : 0.542 12.145 26140 Z= 0.280 Chirality : 0.042 0.336 2902 Planarity : 0.004 0.042 3178 Dihedral : 6.968 56.591 2984 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.49 % Favored : 97.43 % Rotamer: Outliers : 1.82 % Allowed : 23.34 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.18), residues: 2340 helix: 2.47 (0.14), residues: 1310 sheet: -1.55 (0.44), residues: 124 loop : -1.18 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 37 TYR 0.016 0.001 TYR A 695 PHE 0.012 0.001 PHE A 630 TRP 0.011 0.001 TRP F 178 HIS 0.004 0.001 HIS E 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (19372) covalent geometry : angle 0.54118 / 0.28 (26112) SS BOND : bond 0.00324 / 0.23 ( 14) SS BOND : angle 0.94861 / 0.68 ( 28) hydrogen bonds : bond 0.04017 / 2.62 ( 1014) hydrogen bonds : angle 3.69822 / 2.58 ( 2950) Misc. bond : bond 0.00025 / 0.01 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4680 Ramachandran restraints generated. 2340 Oldfield, 0 Emsley, 2340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: A 692 MET cc_start: 0.7737 (mtp) cc_final: 0.7236 (mpp) REVERT: A 743 MET cc_start: 0.6904 (ppp) cc_final: 0.6389 (ppp) REVERT: A 748 ASN cc_start: 0.8023 (m-40) cc_final: 0.7727 (m-40) REVERT: B 495 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7103 (mp0) REVERT: B 592 GLU cc_start: 0.7746 (pm20) cc_final: 0.7481 (pm20) REVERT: B 693 TRP cc_start: 0.7963 (t-100) cc_final: 0.7645 (t-100) REVERT: B 710 GLU cc_start: 0.7581 (tt0) cc_final: 0.7171 (tt0) REVERT: B 719 LYS cc_start: 0.8583 (mttm) cc_final: 0.8179 (mtmm) REVERT: B 737 ARG cc_start: 0.6184 (mmt90) cc_final: 0.5263 (ptm160) REVERT: B 738 LYS cc_start: 0.8604 (pmtt) cc_final: 0.7942 (ttpt) REVERT: E 22 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7333 (p) REVERT: E 37 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.6805 (mmm-85) REVERT: E 95 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6397 (pt0) REVERT: E 126 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7605 (tm-30) REVERT: E 204 ARG cc_start: 0.6967 (mtt-85) cc_final: 0.6559 (mtt90) REVERT: F 22 SER cc_start: 0.7295 (m) cc_final: 0.7086 (m) REVERT: F 37 ARG cc_start: 0.5270 (OUTLIER) cc_final: 0.4698 (mtt-85) REVERT: F 65 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.6973 (ptp90) REVERT: G 12 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7200 (tt) REVERT: G 24 MET cc_start: 0.7393 (tpt) cc_final: 0.6857 (tpt) REVERT: G 95 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6526 (tt0) REVERT: G 106 ILE cc_start: 0.8072 (tt) cc_final: 0.7692 (tp) REVERT: G 126 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7688 (tm-30) REVERT: G 129 LYS cc_start: 0.8641 (mttm) cc_final: 0.8329 (mtmt) REVERT: G 204 ARG cc_start: 0.6922 (mtt-85) cc_final: 0.6563 (mtt90) REVERT: C 478 ASP cc_start: 0.7478 (m-30) cc_final: 0.6866 (t0) REVERT: C 509 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: C 592 GLU cc_start: 0.8335 (pm20) cc_final: 0.7562 (mm-30) REVERT: C 748 ASN cc_start: 0.8354 (m-40) cc_final: 0.8013 (m-40) REVERT: C 810 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8018 (t) REVERT: D 436 MET cc_start: 0.6805 (ptt) cc_final: 0.6467 (pp-130) REVERT: D 441 ASP cc_start: 0.7864 (m-30) cc_final: 0.7362 (t0) REVERT: D 660 ASP cc_start: 0.6777 (m-30) cc_final: 0.6476 (m-30) REVERT: D 683 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7804 (mtm180) REVERT: D 705 THR cc_start: 0.8042 (p) cc_final: 0.7703 (p) REVERT: D 719 LYS cc_start: 0.8588 (mttm) cc_final: 0.7871 (ttpp) REVERT: H 22 SER cc_start: 0.7265 (OUTLIER) cc_final: 0.6897 (m) REVERT: H 31 ASP cc_start: 0.8230 (p0) cc_final: 0.7517 (p0) REVERT: A 1006 GLU cc_start: 0.5635 (mt-10) cc_final: 0.5237 (mm-30) REVERT: C 1006 GLU cc_start: 0.5549 (mm-30) cc_final: 0.5229 (mm-30) outliers start: 35 outliers final: 18 residues processed: 294 average time/residue: 0.6052 time to fit residues: 200.3323 Evaluate side-chains 283 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 679 GLU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 148 SER Chi-restraints excluded: chain H residue 160 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 160 ASN C 434 HIS ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.119756 restraints weight = 53153.918| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.01 r_work: 0.3203 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19390 Z= 0.209 Angle : 0.608 11.523 26140 Z= 0.313 Chirality : 0.044 0.325 2902 Planarity : 0.004 0.040 3178 Dihedral : 7.489 59.408 2984 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 2.02 % Allowed : 23.29 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 2340 helix: 2.14 (0.14), residues: 1318 sheet: -1.86 (0.38), residues: 160 loop : -1.14 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 65 TYR 0.018 0.002 TYR A 695 PHE 0.019 0.002 PHE F 201 TRP 0.011 0.001 TRP B 693 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.21 (19372) covalent geometry : angle 0.60736 / 0.31 (26112) SS BOND : bond 0.00397 / 0.27 ( 14) SS BOND : angle 1.20743 / 0.89 ( 28) hydrogen bonds : bond 0.04840 / 3.15 ( 1014) hydrogen bonds : angle 3.89383 / 2.72 ( 2950) Misc. bond : bond 0.00062 / 0.03 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7638.02 seconds wall clock time: 130 minutes 34.77 seconds (7834.77 seconds total)