Starting phenix.real_space_refine on Sun Feb 18 00:49:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/02_2024/6pqo_20449_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 13360 2.51 5 N 3208 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D ARG 996": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B ARG 996": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C ARG 996": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 278 Unusual residues: {'6OU': 5, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'6OU': 3, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 11.39, per 1000 atoms: 0.56 Number of scatterers: 20312 At special positions: 0 Unit cell: (113.4, 113.4, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 3576 8.00 N 3208 7.00 C 13360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN D 747 " " NAG F 1 " - " ASN A 747 " " NAG G 1 " - " ASN B 747 " " NAG H 1 " - " ASN C 747 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.4 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 485 through 492 removed outlier: 3.674A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 536 Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 610 Processing helix chain 'D' and resid 622 through 629 Processing helix chain 'D' and resid 631 through 641 removed outlier: 3.690A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 713 Processing helix chain 'D' and resid 715 through 738 removed outlier: 3.797A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 817 Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 850 " --> pdb=" O PHE D 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 5.286A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.801A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 926 No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1016 through 1023 Processing helix chain 'D' and resid 1040 through 1071 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 485 through 492 removed outlier: 3.675A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 631 through 641 removed outlier: 3.690A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 684 through 690 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 713 Processing helix chain 'A' and resid 715 through 738 removed outlier: 3.796A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 795 removed outlier: 3.697A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 817 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.707A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 850 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 5.287A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.801A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 926 No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 986 removed outlier: 4.169A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1016 through 1023 Processing helix chain 'A' and resid 1040 through 1071 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.675A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 631 through 641 removed outlier: 3.690A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 713 Processing helix chain 'B' and resid 715 through 738 removed outlier: 3.797A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 817 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 850 " --> pdb=" O PHE B 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 891 removed outlier: 5.287A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.800A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 926 No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1016 through 1023 Processing helix chain 'B' and resid 1040 through 1071 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 485 through 492 removed outlier: 3.675A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 536 Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 610 Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 631 through 641 removed outlier: 3.691A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 713 Processing helix chain 'C' and resid 715 through 738 removed outlier: 3.797A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 817 Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 850 " --> pdb=" O PHE C 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 5.285A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.800A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 926 No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1016 through 1023 Processing helix chain 'C' and resid 1040 through 1071 Processing sheet with id= A, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.001A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= F, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= H, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2913 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: 5.50 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3060 1.30 - 1.43: 5286 1.43 - 1.56: 11863 1.56 - 1.69: 235 1.69 - 1.81: 276 Bond restraints: 20720 Sorted by residual: bond pdb=" C09 JT0 B1204 " pdb=" S21 JT0 B1204 " ideal model delta sigma weight residual 1.543 1.773 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C09 JT0 D1303 " pdb=" S21 JT0 D1303 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C09 JT0 A1204 " pdb=" S21 JT0 A1204 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C09 JT0 C1205 " pdb=" S21 JT0 C1205 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C20 JT0 C1205 " pdb=" S21 JT0 C1205 " ideal model delta sigma weight residual 1.515 1.725 -0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 20715 not shown) Histogram of bond angle deviations from ideal: 89.06 - 98.06: 8 98.06 - 107.06: 700 107.06 - 116.05: 12957 116.05 - 125.05: 13890 125.05 - 134.05: 389 Bond angle restraints: 27944 Sorted by residual: angle pdb=" C18 JT0 B1204 " pdb=" C15 JT0 B1204 " pdb=" O16 JT0 B1204 " ideal model delta sigma weight residual 87.26 120.92 -33.66 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 D1303 " pdb=" C15 JT0 D1303 " pdb=" O16 JT0 D1303 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 C1205 " pdb=" C15 JT0 C1205 " pdb=" O16 JT0 C1205 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 A1204 " pdb=" C15 JT0 A1204 " pdb=" O16 JT0 A1204 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 ... (remaining 27939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 12260 35.43 - 70.86: 328 70.86 - 106.29: 60 106.29 - 141.72: 20 141.72 - 177.15: 12 Dihedral angle restraints: 12680 sinusoidal: 5460 harmonic: 7220 Sorted by residual: dihedral pdb=" C1 LBN A1206 " pdb=" O1 LBN A1206 " pdb=" P1 LBN A1206 " pdb=" O3 LBN A1206 " ideal model delta sinusoidal sigma weight residual 275.40 98.25 177.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN C1207 " pdb=" O1 LBN C1207 " pdb=" P1 LBN C1207 " pdb=" O3 LBN C1207 " ideal model delta sinusoidal sigma weight residual 275.40 98.27 177.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D1305 " pdb=" O1 LBN D1305 " pdb=" P1 LBN D1305 " pdb=" O3 LBN D1305 " ideal model delta sinusoidal sigma weight residual 275.40 98.28 177.12 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 3180 0.182 - 0.364: 8 0.364 - 0.546: 8 0.546 - 0.728: 12 0.728 - 0.910: 4 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.23e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.16e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.15e+01 ... (remaining 3209 not shown) Planarity restraints: 3368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JT0 C1205 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 C1205 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 C1205 " 0.471 2.00e-02 2.50e+03 pdb=" C22 JT0 C1205 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 C1205 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 C1205 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 D1303 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 D1303 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 D1303 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 D1303 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 D1303 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 D1303 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 B1204 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 B1204 " -0.642 2.00e-02 2.50e+03 pdb=" C09 JT0 B1204 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 B1204 " -0.999 2.00e-02 2.50e+03 pdb=" N03 JT0 B1204 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 B1204 " 0.939 2.00e-02 2.50e+03 ... (remaining 3365 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3044 2.76 - 3.29: 18295 3.29 - 3.83: 31504 3.83 - 4.36: 36793 4.36 - 4.90: 63035 Nonbonded interactions: 152671 Sorted by model distance: nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.223 2.520 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.301 2.440 ... (remaining 152666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 446 through 1079 or (resid 1208 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'B' and (resid 446 through 1079 or resid 1208)) selection = (chain 'C' and (resid 446 through 1079 or (resid 1208 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'D' and (resid 446 through 1079 or (resid 1308 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.580 Check model and map are aligned: 0.290 Set scattering table: 0.210 Process input model: 51.420 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 : 0.012 0.230 20720 Z= 0.786 Angle : 1.413 33.663 27944 Z= 0.606 Chirality : 0.079 0.910 3212 Planarity : 0.026 0.651 3364 Dihedral : 18.187 177.148 7984 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 2416 helix: -2.04 (0.10), residues: 1732 sheet: 0.83 (0.76), residues: 68 loop : -1.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 515 HIS 0.011 0.002 HIS A 585 PHE 0.027 0.003 PHE C 783 TYR 0.034 0.003 TYR B 785 ARG 0.015 0.001 ARG C 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 602 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 483 MET cc_start: 0.7988 (mtt) cc_final: 0.7435 (mtm) REVERT: D 558 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7080 (mm-30) REVERT: D 591 LYS cc_start: 0.8962 (mttt) cc_final: 0.8639 (mtmm) REVERT: D 669 PHE cc_start: 0.7510 (m-80) cc_final: 0.7210 (m-80) REVERT: D 717 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6367 (ttt90) REVERT: D 721 MET cc_start: 0.7408 (ttm) cc_final: 0.6878 (mmp) REVERT: D 768 TYR cc_start: 0.7736 (t80) cc_final: 0.7454 (t80) REVERT: D 864 GLU cc_start: 0.7202 (tt0) cc_final: 0.6812 (tt0) REVERT: D 920 GLU cc_start: 0.8021 (tt0) cc_final: 0.7650 (mp0) REVERT: D 924 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 928 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7721 (mtm-85) REVERT: D 963 ASP cc_start: 0.7393 (m-30) cc_final: 0.7112 (m-30) REVERT: D 969 LYS cc_start: 0.7667 (tttt) cc_final: 0.7318 (ttpp) REVERT: D 981 GLU cc_start: 0.7512 (tp30) cc_final: 0.7173 (tp30) REVERT: D 1049 TYR cc_start: 0.8094 (m-10) cc_final: 0.7862 (m-10) REVERT: A 483 MET cc_start: 0.8211 (mtt) cc_final: 0.7670 (mtm) REVERT: A 523 MET cc_start: 0.8180 (tpt) cc_final: 0.7924 (tpt) REVERT: A 558 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7460 (mm-30) REVERT: A 562 LYS cc_start: 0.7755 (mttt) cc_final: 0.7533 (mptp) REVERT: A 579 GLN cc_start: 0.8400 (mt0) cc_final: 0.8195 (mm-40) REVERT: A 591 LYS cc_start: 0.8986 (mttt) cc_final: 0.8701 (mtmm) REVERT: A 657 GLU cc_start: 0.7138 (tt0) cc_final: 0.6866 (tm-30) REVERT: A 669 PHE cc_start: 0.7609 (m-80) cc_final: 0.7290 (m-80) REVERT: A 705 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 717 ARG cc_start: 0.6691 (ttt180) cc_final: 0.6120 (ttt90) REVERT: A 720 MET cc_start: 0.6859 (mmm) cc_final: 0.6626 (mmm) REVERT: A 721 MET cc_start: 0.7208 (ttm) cc_final: 0.6760 (mmp) REVERT: A 768 TYR cc_start: 0.7747 (t80) cc_final: 0.7424 (t80) REVERT: A 825 GLU cc_start: 0.8246 (tt0) cc_final: 0.7991 (tm-30) REVERT: A 852 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7456 (mmt90) REVERT: A 864 GLU cc_start: 0.7065 (tt0) cc_final: 0.6701 (tt0) REVERT: A 920 GLU cc_start: 0.8278 (tt0) cc_final: 0.7464 (mp0) REVERT: A 924 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 928 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7853 (mtm-85) REVERT: A 981 GLU cc_start: 0.7438 (tp30) cc_final: 0.7113 (tp30) REVERT: A 1042 MET cc_start: 0.7190 (ppp) cc_final: 0.6736 (mmp) REVERT: A 1049 TYR cc_start: 0.8057 (m-10) cc_final: 0.7843 (m-10) REVERT: A 1050 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7319 (ttm110) REVERT: B 483 MET cc_start: 0.8033 (mtt) cc_final: 0.7497 (mtm) REVERT: B 523 MET cc_start: 0.7845 (tpt) cc_final: 0.7581 (tpt) REVERT: B 558 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 562 LYS cc_start: 0.7720 (mttt) cc_final: 0.7512 (mptp) REVERT: B 591 LYS cc_start: 0.8970 (mttt) cc_final: 0.8683 (mtmm) REVERT: B 603 LYS cc_start: 0.8817 (mttt) cc_final: 0.8592 (mtpt) REVERT: B 657 GLU cc_start: 0.7116 (tt0) cc_final: 0.6841 (tm-30) REVERT: B 669 PHE cc_start: 0.7651 (m-80) cc_final: 0.7225 (m-80) REVERT: B 689 MET cc_start: 0.7853 (mtm) cc_final: 0.7648 (mtp) REVERT: B 705 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6940 (mm-30) REVERT: B 717 ARG cc_start: 0.6742 (ttt180) cc_final: 0.6213 (ttt90) REVERT: B 720 MET cc_start: 0.6809 (mmm) cc_final: 0.6550 (mmm) REVERT: B 721 MET cc_start: 0.7262 (ttm) cc_final: 0.6729 (mmp) REVERT: B 768 TYR cc_start: 0.7864 (t80) cc_final: 0.7540 (t80) REVERT: B 825 GLU cc_start: 0.8299 (tt0) cc_final: 0.8050 (tm-30) REVERT: B 864 GLU cc_start: 0.7171 (tt0) cc_final: 0.6791 (tt0) REVERT: B 920 GLU cc_start: 0.8171 (tt0) cc_final: 0.7661 (mp0) REVERT: B 924 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 963 ASP cc_start: 0.7550 (m-30) cc_final: 0.7282 (m-30) REVERT: B 969 LYS cc_start: 0.7734 (tttt) cc_final: 0.7385 (ttpp) REVERT: B 981 GLU cc_start: 0.7420 (tp30) cc_final: 0.7096 (tp30) REVERT: B 1049 TYR cc_start: 0.8148 (m-10) cc_final: 0.7869 (m-10) REVERT: B 1050 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7234 (ttm110) REVERT: C 562 LYS cc_start: 0.8349 (mttt) cc_final: 0.8093 (mptp) REVERT: C 571 ASN cc_start: 0.8525 (m110) cc_final: 0.8290 (m-40) REVERT: C 591 LYS cc_start: 0.8983 (mttt) cc_final: 0.8739 (mttm) REVERT: C 594 GLU cc_start: 0.7774 (tp30) cc_final: 0.7313 (tp30) REVERT: C 630 LEU cc_start: 0.8077 (mt) cc_final: 0.7823 (mt) REVERT: C 635 LYS cc_start: 0.7137 (tttt) cc_final: 0.6776 (tptm) REVERT: C 699 ASN cc_start: 0.8293 (m-40) cc_final: 0.8009 (m-40) REVERT: C 704 LYS cc_start: 0.7073 (mttt) cc_final: 0.6801 (mtpp) REVERT: C 719 HIS cc_start: 0.6772 (t-90) cc_final: 0.6550 (t70) REVERT: C 720 MET cc_start: 0.7096 (mmm) cc_final: 0.6677 (mmm) REVERT: C 768 TYR cc_start: 0.8179 (t80) cc_final: 0.7900 (t80) REVERT: C 825 GLU cc_start: 0.7973 (tt0) cc_final: 0.7601 (tm-30) REVERT: C 852 ARG cc_start: 0.7544 (mtt90) cc_final: 0.7240 (mmt90) REVERT: C 864 GLU cc_start: 0.7215 (tt0) cc_final: 0.7000 (tt0) REVERT: C 900 SER cc_start: 0.8421 (m) cc_final: 0.8082 (t) REVERT: C 969 LYS cc_start: 0.7641 (tttt) cc_final: 0.7264 (ttpp) REVERT: C 1050 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6905 (ttp-110) REVERT: C 1073 GLU cc_start: 0.7748 (tt0) cc_final: 0.7547 (tt0) outliers start: 12 outliers final: 3 residues processed: 610 average time/residue: 1.3241 time to fit residues: 908.3432 Evaluate side-chains 312 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain B residue 465 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 451 HIS D 512 HIS D 519 HIS D 549 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN A 451 HIS A 460 ASN A 512 HIS A 519 HIS A 549 ASN A 644 HIS A 700 HIS A 719 HIS A 851 GLN A 970 HIS B 451 HIS B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 851 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 512 HIS C 519 HIS C 570 HIS C 577 ASN C 644 HIS C 700 HIS C 719 HIS C 739 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20720 Z= 0.223 Angle : 0.633 9.215 27944 Z= 0.302 Chirality : 0.041 0.148 3212 Planarity : 0.005 0.058 3364 Dihedral : 19.286 155.896 3518 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.99 % Allowed : 12.79 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2416 helix: -0.29 (0.12), residues: 1712 sheet: 1.41 (0.73), residues: 68 loop : -0.87 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 515 HIS 0.006 0.001 HIS D 585 PHE 0.013 0.001 PHE C 823 TYR 0.017 0.001 TYR A 785 ARG 0.006 0.001 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 317 time to evaluate : 2.156 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8010 (mtt) cc_final: 0.7576 (mtm) REVERT: D 547 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7080 (t0) REVERT: D 591 LYS cc_start: 0.8903 (mttt) cc_final: 0.8638 (mtmm) REVERT: D 669 PHE cc_start: 0.7597 (m-80) cc_final: 0.7213 (m-80) REVERT: D 717 ARG cc_start: 0.6743 (ttt180) cc_final: 0.6230 (ttt90) REVERT: D 721 MET cc_start: 0.7155 (ttm) cc_final: 0.6765 (mmp) REVERT: D 768 TYR cc_start: 0.7736 (t80) cc_final: 0.7402 (t80) REVERT: D 920 GLU cc_start: 0.8029 (tt0) cc_final: 0.7713 (mp0) REVERT: D 969 LYS cc_start: 0.7367 (tttt) cc_final: 0.6960 (ttpp) REVERT: D 981 GLU cc_start: 0.7374 (tp30) cc_final: 0.7087 (tp30) REVERT: D 1049 TYR cc_start: 0.7928 (m-10) cc_final: 0.7701 (m-10) REVERT: D 1050 ARG cc_start: 0.7384 (ttm-80) cc_final: 0.7183 (mtp85) REVERT: A 483 MET cc_start: 0.7916 (mtt) cc_final: 0.7684 (mtm) REVERT: A 544 LEU cc_start: 0.8570 (mt) cc_final: 0.8264 (mm) REVERT: A 591 LYS cc_start: 0.8906 (mttt) cc_final: 0.8571 (mtmm) REVERT: A 669 PHE cc_start: 0.7732 (m-80) cc_final: 0.7392 (m-80) REVERT: A 696 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: A 717 ARG cc_start: 0.6632 (ttt180) cc_final: 0.6098 (ttt90) REVERT: A 720 MET cc_start: 0.6761 (mmm) cc_final: 0.6520 (mmm) REVERT: A 721 MET cc_start: 0.7150 (ttm) cc_final: 0.6746 (mmp) REVERT: A 744 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7143 (mtt) REVERT: A 768 TYR cc_start: 0.7910 (t80) cc_final: 0.7613 (t80) REVERT: A 808 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7140 (mp0) REVERT: A 825 GLU cc_start: 0.8249 (tt0) cc_final: 0.8002 (tm-30) REVERT: A 852 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7577 (mmt90) REVERT: A 864 GLU cc_start: 0.7126 (tt0) cc_final: 0.6917 (tt0) REVERT: A 920 GLU cc_start: 0.8150 (tt0) cc_final: 0.7553 (mp0) REVERT: A 928 ARG cc_start: 0.8129 (mtm180) cc_final: 0.7890 (mtm-85) REVERT: A 981 GLU cc_start: 0.7407 (tp30) cc_final: 0.7140 (tp30) REVERT: A 1050 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.6998 (ttp-110) REVERT: A 1063 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: B 483 MET cc_start: 0.8050 (mtt) cc_final: 0.7562 (mtm) REVERT: B 547 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7023 (t0) REVERT: B 591 LYS cc_start: 0.8892 (mttt) cc_final: 0.8625 (mtmm) REVERT: B 603 LYS cc_start: 0.8948 (mttt) cc_final: 0.8724 (mtpt) REVERT: B 669 PHE cc_start: 0.7661 (m-80) cc_final: 0.7260 (m-80) REVERT: B 717 ARG cc_start: 0.6644 (ttt180) cc_final: 0.6143 (ttt90) REVERT: B 720 MET cc_start: 0.6680 (mmm) cc_final: 0.6424 (mmm) REVERT: B 721 MET cc_start: 0.7172 (ttm) cc_final: 0.6663 (mmp) REVERT: B 768 TYR cc_start: 0.7985 (t80) cc_final: 0.7665 (t80) REVERT: B 825 GLU cc_start: 0.8302 (tt0) cc_final: 0.8050 (tm-30) REVERT: B 864 GLU cc_start: 0.7120 (tt0) cc_final: 0.6790 (tt0) REVERT: B 920 GLU cc_start: 0.8010 (tt0) cc_final: 0.7614 (mp0) REVERT: B 981 GLU cc_start: 0.7413 (tp30) cc_final: 0.7130 (tp30) REVERT: B 1049 TYR cc_start: 0.8009 (m-10) cc_final: 0.7740 (m-10) REVERT: B 1050 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.7165 (ttm110) REVERT: C 544 LEU cc_start: 0.8441 (mt) cc_final: 0.7933 (mm) REVERT: C 571 ASN cc_start: 0.8533 (m110) cc_final: 0.8326 (m-40) REVERT: C 591 LYS cc_start: 0.8944 (mttt) cc_final: 0.8715 (mttp) REVERT: C 594 GLU cc_start: 0.7791 (tp30) cc_final: 0.7213 (tp30) REVERT: C 669 PHE cc_start: 0.7541 (m-80) cc_final: 0.6806 (m-80) REVERT: C 704 LYS cc_start: 0.7015 (mttt) cc_final: 0.6756 (mttp) REVERT: C 719 HIS cc_start: 0.6867 (t70) cc_final: 0.6505 (t70) REVERT: C 768 TYR cc_start: 0.8032 (t80) cc_final: 0.7789 (t80) REVERT: C 825 GLU cc_start: 0.7968 (tt0) cc_final: 0.7633 (tm-30) REVERT: C 852 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7334 (mmt90) REVERT: C 920 GLU cc_start: 0.7876 (tt0) cc_final: 0.7584 (mp0) REVERT: C 974 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7081 (tmtt) REVERT: C 981 GLU cc_start: 0.7303 (tp30) cc_final: 0.6878 (tm-30) REVERT: C 1000 GLN cc_start: 0.8390 (mt0) cc_final: 0.7760 (mm110) REVERT: C 1073 GLU cc_start: 0.7734 (tt0) cc_final: 0.7520 (tt0) outliers start: 82 outliers final: 29 residues processed: 381 average time/residue: 1.3084 time to fit residues: 562.5585 Evaluate side-chains 302 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 267 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 974 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.0870 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 460 ASN D 691 GLN D 907 GLN D 983 HIS A 687 ASN A 805 ASN A 907 GLN A 983 HIS B 460 ASN B 691 GLN B 855 ASN B 907 GLN B 970 HIS B 983 HIS C 463 GLN C 577 ASN C 805 ASN C 970 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20720 Z= 0.236 Angle : 0.578 7.598 27944 Z= 0.284 Chirality : 0.041 0.162 3212 Planarity : 0.004 0.058 3364 Dihedral : 17.558 162.834 3512 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.52 % Allowed : 14.01 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2416 helix: 0.59 (0.12), residues: 1716 sheet: 2.65 (0.84), residues: 48 loop : -0.71 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 515 HIS 0.007 0.001 HIS B 494 PHE 0.013 0.002 PHE C 583 TYR 0.019 0.002 TYR A 785 ARG 0.006 0.001 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 288 time to evaluate : 2.423 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.8646 (mt) cc_final: 0.8311 (mm) REVERT: D 547 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7093 (t0) REVERT: D 591 LYS cc_start: 0.8865 (mttt) cc_final: 0.8590 (mtmm) REVERT: D 634 MET cc_start: 0.7347 (tpt) cc_final: 0.7102 (tpt) REVERT: D 669 PHE cc_start: 0.7796 (m-80) cc_final: 0.7371 (m-80) REVERT: D 717 ARG cc_start: 0.6708 (ttt180) cc_final: 0.6263 (ttt90) REVERT: D 721 MET cc_start: 0.7168 (ttm) cc_final: 0.6775 (mmp) REVERT: D 744 MET cc_start: 0.7218 (mtp) cc_final: 0.6953 (mtp) REVERT: D 768 TYR cc_start: 0.7524 (t80) cc_final: 0.7261 (t80) REVERT: D 864 GLU cc_start: 0.7038 (tt0) cc_final: 0.6837 (tt0) REVERT: D 920 GLU cc_start: 0.7834 (tt0) cc_final: 0.7524 (mp0) REVERT: D 981 GLU cc_start: 0.7334 (tp30) cc_final: 0.7016 (tp30) REVERT: A 483 MET cc_start: 0.7917 (mtt) cc_final: 0.7515 (mmm) REVERT: A 544 LEU cc_start: 0.8620 (mt) cc_final: 0.8272 (mm) REVERT: A 578 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7082 (ttmm) REVERT: A 591 LYS cc_start: 0.8892 (mttt) cc_final: 0.8589 (mtmm) REVERT: A 669 PHE cc_start: 0.7764 (m-80) cc_final: 0.7354 (m-80) REVERT: A 717 ARG cc_start: 0.6664 (ttt180) cc_final: 0.6149 (ttt90) REVERT: A 721 MET cc_start: 0.7026 (ttm) cc_final: 0.6651 (mmp) REVERT: A 744 MET cc_start: 0.7335 (mtp) cc_final: 0.7025 (mtp) REVERT: A 768 TYR cc_start: 0.7763 (t80) cc_final: 0.7468 (t80) REVERT: A 825 GLU cc_start: 0.8224 (tt0) cc_final: 0.7999 (tm-30) REVERT: A 852 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7585 (mmt90) REVERT: A 920 GLU cc_start: 0.7982 (tt0) cc_final: 0.7687 (mp0) REVERT: A 981 GLU cc_start: 0.7341 (tp30) cc_final: 0.7117 (tp30) REVERT: A 987 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: A 1049 TYR cc_start: 0.8091 (m-10) cc_final: 0.7886 (m-10) REVERT: A 1063 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: B 544 LEU cc_start: 0.8639 (mt) cc_final: 0.8278 (mm) REVERT: B 547 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6998 (t0) REVERT: B 591 LYS cc_start: 0.8878 (mttt) cc_final: 0.8603 (mtmm) REVERT: B 603 LYS cc_start: 0.8988 (mttt) cc_final: 0.8710 (mtmp) REVERT: B 634 MET cc_start: 0.7256 (tpt) cc_final: 0.7009 (tpt) REVERT: B 669 PHE cc_start: 0.7802 (m-80) cc_final: 0.7385 (m-80) REVERT: B 717 ARG cc_start: 0.6693 (ttt180) cc_final: 0.6247 (ttt90) REVERT: B 721 MET cc_start: 0.7077 (ttm) cc_final: 0.6596 (mmp) REVERT: B 768 TYR cc_start: 0.7722 (t80) cc_final: 0.7467 (t80) REVERT: B 825 GLU cc_start: 0.8267 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 920 GLU cc_start: 0.7923 (tt0) cc_final: 0.7605 (mp0) REVERT: B 981 GLU cc_start: 0.7329 (tp30) cc_final: 0.7118 (tp30) REVERT: C 544 LEU cc_start: 0.8444 (mt) cc_final: 0.8061 (mm) REVERT: C 604 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.5647 (mtm-85) REVERT: C 669 PHE cc_start: 0.7620 (m-80) cc_final: 0.6978 (m-80) REVERT: C 704 LYS cc_start: 0.6894 (mttt) cc_final: 0.6637 (mttp) REVERT: C 768 TYR cc_start: 0.7900 (t80) cc_final: 0.7613 (t80) REVERT: C 825 GLU cc_start: 0.8067 (tt0) cc_final: 0.7743 (tm-30) REVERT: C 852 ARG cc_start: 0.7591 (mtt90) cc_final: 0.7226 (mtt90) REVERT: C 920 GLU cc_start: 0.7753 (tt0) cc_final: 0.7472 (mp0) REVERT: C 981 GLU cc_start: 0.7460 (tp30) cc_final: 0.7174 (tp30) REVERT: C 1000 GLN cc_start: 0.8221 (mt0) cc_final: 0.7800 (mm110) REVERT: C 1059 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7086 (mt-10) REVERT: C 1063 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: C 1073 GLU cc_start: 0.7938 (tt0) cc_final: 0.7701 (tt0) outliers start: 93 outliers final: 33 residues processed: 359 average time/residue: 1.2758 time to fit residues: 518.0354 Evaluate side-chains 299 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 987 GLU Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 687 ASN D 691 GLN D 970 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 983 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20720 Z= 0.235 Angle : 0.539 7.086 27944 Z= 0.269 Chirality : 0.040 0.169 3212 Planarity : 0.004 0.056 3364 Dihedral : 16.991 164.108 3512 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.94 % Allowed : 15.95 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2416 helix: 0.94 (0.13), residues: 1720 sheet: 2.77 (0.83), residues: 48 loop : -0.53 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 515 HIS 0.005 0.001 HIS D 585 PHE 0.011 0.001 PHE C 583 TYR 0.016 0.001 TYR A 785 ARG 0.004 0.001 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 270 time to evaluate : 2.251 Fit side-chains revert: symmetry clash REVERT: D 544 LEU cc_start: 0.8646 (mt) cc_final: 0.8305 (mm) REVERT: D 547 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7093 (t0) REVERT: D 591 LYS cc_start: 0.8837 (mttt) cc_final: 0.8585 (mtmm) REVERT: D 669 PHE cc_start: 0.7829 (m-80) cc_final: 0.7416 (m-80) REVERT: D 717 ARG cc_start: 0.6697 (ttt180) cc_final: 0.6240 (ttt90) REVERT: D 721 MET cc_start: 0.7063 (ttm) cc_final: 0.6663 (mmp) REVERT: D 744 MET cc_start: 0.7321 (mtp) cc_final: 0.7056 (mtp) REVERT: D 768 TYR cc_start: 0.7579 (t80) cc_final: 0.7334 (t80) REVERT: D 864 GLU cc_start: 0.7051 (tt0) cc_final: 0.6781 (tt0) REVERT: D 872 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6953 (mtp180) REVERT: D 920 GLU cc_start: 0.7777 (tt0) cc_final: 0.7508 (mp0) REVERT: D 981 GLU cc_start: 0.7341 (tp30) cc_final: 0.7019 (tp30) REVERT: A 483 MET cc_start: 0.7937 (mtt) cc_final: 0.7574 (mmm) REVERT: A 544 LEU cc_start: 0.8613 (mt) cc_final: 0.8246 (mm) REVERT: A 578 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7184 (tppt) REVERT: A 579 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7921 (mm-40) REVERT: A 591 LYS cc_start: 0.8884 (mttt) cc_final: 0.8575 (mtmm) REVERT: A 669 PHE cc_start: 0.7817 (m-80) cc_final: 0.7407 (m-80) REVERT: A 717 ARG cc_start: 0.6713 (ttt180) cc_final: 0.6202 (ttt90) REVERT: A 721 MET cc_start: 0.7049 (ttm) cc_final: 0.6647 (mmp) REVERT: A 744 MET cc_start: 0.7289 (mtp) cc_final: 0.6972 (mtp) REVERT: A 768 TYR cc_start: 0.7766 (t80) cc_final: 0.7492 (t80) REVERT: A 808 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7162 (mp0) REVERT: A 825 GLU cc_start: 0.8212 (tt0) cc_final: 0.7983 (tm-30) REVERT: A 852 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7602 (mmt90) REVERT: A 920 GLU cc_start: 0.7909 (tt0) cc_final: 0.7658 (mp0) REVERT: A 981 GLU cc_start: 0.7332 (tp30) cc_final: 0.7119 (tp30) REVERT: A 1063 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: B 544 LEU cc_start: 0.8647 (mt) cc_final: 0.8272 (mm) REVERT: B 547 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6992 (t0) REVERT: B 591 LYS cc_start: 0.8863 (mttt) cc_final: 0.8605 (mtmm) REVERT: B 603 LYS cc_start: 0.9029 (mttt) cc_final: 0.8695 (mtmp) REVERT: B 634 MET cc_start: 0.7336 (tpt) cc_final: 0.7123 (tpt) REVERT: B 669 PHE cc_start: 0.7807 (m-80) cc_final: 0.7374 (m-80) REVERT: B 717 ARG cc_start: 0.6719 (ttt180) cc_final: 0.6258 (ttt90) REVERT: B 721 MET cc_start: 0.7090 (ttm) cc_final: 0.6648 (mmp) REVERT: B 768 TYR cc_start: 0.7708 (t80) cc_final: 0.7505 (t80) REVERT: B 825 GLU cc_start: 0.8249 (tt0) cc_final: 0.7999 (tm-30) REVERT: B 855 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7707 (OUTLIER) REVERT: B 920 GLU cc_start: 0.7793 (tt0) cc_final: 0.7516 (mp0) REVERT: B 981 GLU cc_start: 0.7322 (tp30) cc_final: 0.7106 (tp30) REVERT: C 544 LEU cc_start: 0.8540 (mt) cc_final: 0.8134 (mm) REVERT: C 604 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5639 (mtm-85) REVERT: C 606 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: C 669 PHE cc_start: 0.7649 (m-80) cc_final: 0.7020 (m-80) REVERT: C 768 TYR cc_start: 0.7936 (t80) cc_final: 0.7621 (t80) REVERT: C 808 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7037 (mp0) REVERT: C 825 GLU cc_start: 0.8081 (tt0) cc_final: 0.7773 (tm-30) REVERT: C 852 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7375 (mtt90) REVERT: C 920 GLU cc_start: 0.7731 (tt0) cc_final: 0.7464 (mp0) REVERT: C 981 GLU cc_start: 0.7488 (tp30) cc_final: 0.7200 (tp30) REVERT: C 1000 GLN cc_start: 0.8269 (mt0) cc_final: 0.7763 (mm110) REVERT: C 1063 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6450 (mp0) outliers start: 81 outliers final: 41 residues processed: 321 average time/residue: 1.4165 time to fit residues: 510.3618 Evaluate side-chains 306 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 257 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain D residue 872 ARG Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 211 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B 691 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20720 Z= 0.145 Angle : 0.484 6.840 27944 Z= 0.243 Chirality : 0.038 0.170 3212 Planarity : 0.004 0.055 3364 Dihedral : 16.327 168.881 3512 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 16.29 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2416 helix: 1.25 (0.13), residues: 1728 sheet: 2.91 (0.82), residues: 48 loop : -0.57 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 832 HIS 0.004 0.001 HIS D 585 PHE 0.008 0.001 PHE C 612 TYR 0.010 0.001 TYR B 785 ARG 0.004 0.000 ARG D1050 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 275 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: D 483 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7853 (mtm) REVERT: D 544 LEU cc_start: 0.8642 (mt) cc_final: 0.8294 (mm) REVERT: D 547 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7078 (t0) REVERT: D 591 LYS cc_start: 0.8846 (mttt) cc_final: 0.8550 (mtmm) REVERT: D 669 PHE cc_start: 0.7837 (m-80) cc_final: 0.7420 (m-80) REVERT: D 717 ARG cc_start: 0.6692 (ttt180) cc_final: 0.6231 (ttt90) REVERT: D 721 MET cc_start: 0.7015 (ttm) cc_final: 0.6637 (mmp) REVERT: D 744 MET cc_start: 0.7285 (mtp) cc_final: 0.7021 (mtp) REVERT: D 768 TYR cc_start: 0.7478 (t80) cc_final: 0.7209 (t80) REVERT: D 864 GLU cc_start: 0.7078 (tt0) cc_final: 0.6854 (tt0) REVERT: D 920 GLU cc_start: 0.7733 (tt0) cc_final: 0.7508 (mp0) REVERT: D 981 GLU cc_start: 0.7341 (tp30) cc_final: 0.7039 (tp30) REVERT: A 483 MET cc_start: 0.7920 (mtt) cc_final: 0.7581 (mmm) REVERT: A 544 LEU cc_start: 0.8652 (mt) cc_final: 0.8320 (mm) REVERT: A 591 LYS cc_start: 0.8868 (mttt) cc_final: 0.8578 (mtmm) REVERT: A 669 PHE cc_start: 0.7819 (m-80) cc_final: 0.7408 (m-80) REVERT: A 717 ARG cc_start: 0.6664 (ttt180) cc_final: 0.6137 (ttt90) REVERT: A 721 MET cc_start: 0.7007 (ttm) cc_final: 0.6635 (mmp) REVERT: A 744 MET cc_start: 0.7301 (mtp) cc_final: 0.7047 (mtp) REVERT: A 768 TYR cc_start: 0.7604 (t80) cc_final: 0.7390 (t80) REVERT: A 825 GLU cc_start: 0.8212 (tt0) cc_final: 0.7962 (tm-30) REVERT: A 852 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7649 (mmt90) REVERT: A 881 LEU cc_start: 0.7679 (tp) cc_final: 0.7185 (tp) REVERT: A 920 GLU cc_start: 0.7887 (tt0) cc_final: 0.7605 (mp0) REVERT: A 981 GLU cc_start: 0.7349 (tp30) cc_final: 0.7070 (tp30) REVERT: A 1059 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 1063 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: B 483 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7628 (mmm) REVERT: B 544 LEU cc_start: 0.8660 (mt) cc_final: 0.8296 (mm) REVERT: B 547 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6956 (t0) REVERT: B 591 LYS cc_start: 0.8859 (mttt) cc_final: 0.8556 (mtmm) REVERT: B 603 LYS cc_start: 0.9013 (mttt) cc_final: 0.8704 (mtmp) REVERT: B 634 MET cc_start: 0.7327 (tpt) cc_final: 0.7100 (tpt) REVERT: B 669 PHE cc_start: 0.7812 (m-80) cc_final: 0.7366 (m-80) REVERT: B 717 ARG cc_start: 0.6648 (ttt180) cc_final: 0.6205 (ttt90) REVERT: B 721 MET cc_start: 0.7021 (ttm) cc_final: 0.6625 (mmp) REVERT: B 808 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7048 (mp0) REVERT: B 825 GLU cc_start: 0.8236 (tt0) cc_final: 0.7988 (tm-30) REVERT: B 920 GLU cc_start: 0.7777 (tt0) cc_final: 0.7528 (mp0) REVERT: B 981 GLU cc_start: 0.7323 (tp30) cc_final: 0.7054 (tp30) REVERT: C 544 LEU cc_start: 0.8545 (mt) cc_final: 0.8131 (mm) REVERT: C 604 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.5647 (mtm-85) REVERT: C 606 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: C 669 PHE cc_start: 0.7782 (m-80) cc_final: 0.7140 (m-80) REVERT: C 768 TYR cc_start: 0.7818 (t80) cc_final: 0.7617 (t80) REVERT: C 825 GLU cc_start: 0.8094 (tt0) cc_final: 0.7786 (tm-30) REVERT: C 852 ARG cc_start: 0.7677 (mtt90) cc_final: 0.7436 (mtt90) REVERT: C 920 GLU cc_start: 0.7724 (tt0) cc_final: 0.7461 (mp0) REVERT: C 981 GLU cc_start: 0.7435 (tp30) cc_final: 0.7161 (tp30) REVERT: C 1000 GLN cc_start: 0.8320 (mt0) cc_final: 0.7835 (mm110) REVERT: C 1063 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6440 (mp0) outliers start: 78 outliers final: 22 residues processed: 329 average time/residue: 1.3114 time to fit residues: 487.1460 Evaluate side-chains 283 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 547 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 0.2980 chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 HIS D 570 HIS D 855 ASN A 519 HIS A 570 HIS A 855 ASN B 519 HIS B 570 HIS B 855 ASN C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS C 907 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20720 Z= 0.268 Angle : 0.555 6.598 27944 Z= 0.277 Chirality : 0.041 0.174 3212 Planarity : 0.004 0.054 3364 Dihedral : 16.014 167.433 3512 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.89 % Allowed : 17.32 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2416 helix: 1.24 (0.13), residues: 1728 sheet: 2.92 (0.82), residues: 48 loop : -0.59 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 515 HIS 0.006 0.001 HIS D 585 PHE 0.011 0.002 PHE B 583 TYR 0.012 0.001 TYR B 785 ARG 0.004 0.001 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 258 time to evaluate : 2.280 Fit side-chains REVERT: D 483 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7697 (mtp) REVERT: D 544 LEU cc_start: 0.8689 (mt) cc_final: 0.8319 (mm) REVERT: D 547 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7063 (t0) REVERT: D 591 LYS cc_start: 0.8868 (mttt) cc_final: 0.8630 (mtmm) REVERT: D 669 PHE cc_start: 0.7845 (m-80) cc_final: 0.7362 (m-80) REVERT: D 681 GLU cc_start: 0.8151 (pt0) cc_final: 0.7577 (pt0) REVERT: D 717 ARG cc_start: 0.6824 (ttt180) cc_final: 0.6349 (ttt90) REVERT: D 721 MET cc_start: 0.7081 (ttm) cc_final: 0.6659 (mmp) REVERT: D 744 MET cc_start: 0.7341 (mtp) cc_final: 0.7003 (mtp) REVERT: D 768 TYR cc_start: 0.7627 (t80) cc_final: 0.7402 (t80) REVERT: D 864 GLU cc_start: 0.7059 (tt0) cc_final: 0.6777 (tt0) REVERT: D 920 GLU cc_start: 0.7704 (tt0) cc_final: 0.7449 (mp0) REVERT: D 966 GLU cc_start: 0.4846 (tp30) cc_final: 0.4606 (mm-30) REVERT: D 981 GLU cc_start: 0.7359 (tp30) cc_final: 0.7106 (tp30) REVERT: A 483 MET cc_start: 0.7933 (mtt) cc_final: 0.7591 (mmm) REVERT: A 544 LEU cc_start: 0.8671 (mt) cc_final: 0.8306 (mm) REVERT: A 578 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7239 (ttmm) REVERT: A 591 LYS cc_start: 0.8854 (mttt) cc_final: 0.8545 (mtmm) REVERT: A 669 PHE cc_start: 0.7851 (m-80) cc_final: 0.7413 (m-80) REVERT: A 681 GLU cc_start: 0.8065 (pt0) cc_final: 0.7486 (pt0) REVERT: A 717 ARG cc_start: 0.6735 (ttt180) cc_final: 0.6252 (ttt90) REVERT: A 721 MET cc_start: 0.7064 (ttm) cc_final: 0.6661 (mmp) REVERT: A 744 MET cc_start: 0.7396 (mtp) cc_final: 0.7003 (mtp) REVERT: A 768 TYR cc_start: 0.7692 (t80) cc_final: 0.7490 (t80) REVERT: A 808 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7130 (mp0) REVERT: A 825 GLU cc_start: 0.8212 (tt0) cc_final: 0.7999 (tm-30) REVERT: A 852 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7617 (mmt90) REVERT: A 920 GLU cc_start: 0.7761 (tt0) cc_final: 0.7463 (mp0) REVERT: A 981 GLU cc_start: 0.7357 (tp30) cc_final: 0.7071 (tp30) REVERT: A 1063 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: B 483 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7639 (mtp) REVERT: B 544 LEU cc_start: 0.8682 (mt) cc_final: 0.8293 (mm) REVERT: B 591 LYS cc_start: 0.8844 (mttt) cc_final: 0.8606 (mtmm) REVERT: B 603 LYS cc_start: 0.9074 (mttt) cc_final: 0.8718 (mtmp) REVERT: B 669 PHE cc_start: 0.7851 (m-80) cc_final: 0.7387 (m-80) REVERT: B 717 ARG cc_start: 0.6828 (ttt180) cc_final: 0.6334 (ttt90) REVERT: B 721 MET cc_start: 0.7100 (ttm) cc_final: 0.6648 (mmp) REVERT: B 808 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7172 (mp0) REVERT: B 825 GLU cc_start: 0.8210 (tt0) cc_final: 0.7974 (tm-30) REVERT: B 920 GLU cc_start: 0.7712 (tt0) cc_final: 0.7456 (mp0) REVERT: B 966 GLU cc_start: 0.4836 (tp30) cc_final: 0.4613 (mm-30) REVERT: B 981 GLU cc_start: 0.7352 (tp30) cc_final: 0.7064 (tp30) REVERT: C 544 LEU cc_start: 0.8555 (mt) cc_final: 0.8121 (mm) REVERT: C 604 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.5729 (mtm-85) REVERT: C 606 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: C 669 PHE cc_start: 0.7876 (m-80) cc_final: 0.7270 (m-80) REVERT: C 808 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7135 (mp0) REVERT: C 825 GLU cc_start: 0.8129 (tt0) cc_final: 0.7853 (tm-30) REVERT: C 852 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7463 (mtt90) REVERT: C 920 GLU cc_start: 0.7695 (tt0) cc_final: 0.7452 (mp0) REVERT: C 1000 GLN cc_start: 0.8239 (mt0) cc_final: 0.7651 (mm110) REVERT: C 1063 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6545 (mp0) outliers start: 80 outliers final: 39 residues processed: 308 average time/residue: 1.3000 time to fit residues: 453.6563 Evaluate side-chains 298 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 251 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 615 ASN Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 787 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 719 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS A 855 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20720 Z= 0.158 Angle : 0.497 6.996 27944 Z= 0.250 Chirality : 0.038 0.149 3212 Planarity : 0.004 0.052 3364 Dihedral : 15.800 170.178 3512 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.31 % Allowed : 18.29 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2416 helix: 1.42 (0.13), residues: 1732 sheet: 3.02 (0.82), residues: 48 loop : -0.50 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 832 HIS 0.003 0.001 HIS D 585 PHE 0.008 0.001 PHE B 583 TYR 0.008 0.001 TYR B 785 ARG 0.004 0.000 ARG D 852 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 260 time to evaluate : 1.974 Fit side-chains REVERT: D 483 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7751 (mtp) REVERT: D 544 LEU cc_start: 0.8685 (mt) cc_final: 0.8321 (mm) REVERT: D 547 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7044 (t0) REVERT: D 591 LYS cc_start: 0.8887 (mttt) cc_final: 0.8641 (mtmm) REVERT: D 669 PHE cc_start: 0.7857 (m-80) cc_final: 0.7373 (m-80) REVERT: D 681 GLU cc_start: 0.8071 (pt0) cc_final: 0.7491 (pt0) REVERT: D 717 ARG cc_start: 0.6720 (ttt180) cc_final: 0.6272 (ttt90) REVERT: D 721 MET cc_start: 0.7034 (ttm) cc_final: 0.6629 (mmp) REVERT: D 744 MET cc_start: 0.7355 (mtp) cc_final: 0.7080 (mtp) REVERT: D 768 TYR cc_start: 0.7564 (t80) cc_final: 0.7343 (t80) REVERT: D 864 GLU cc_start: 0.7092 (tt0) cc_final: 0.6838 (tt0) REVERT: D 920 GLU cc_start: 0.7653 (tt0) cc_final: 0.7439 (mp0) REVERT: D 981 GLU cc_start: 0.7357 (tp30) cc_final: 0.7053 (tp30) REVERT: A 483 MET cc_start: 0.8039 (mtt) cc_final: 0.7703 (mmm) REVERT: A 544 LEU cc_start: 0.8653 (mt) cc_final: 0.8294 (mm) REVERT: A 591 LYS cc_start: 0.8860 (mttt) cc_final: 0.8559 (mtmm) REVERT: A 669 PHE cc_start: 0.7855 (m-80) cc_final: 0.7416 (m-80) REVERT: A 717 ARG cc_start: 0.6689 (ttt180) cc_final: 0.6216 (ttt90) REVERT: A 721 MET cc_start: 0.7013 (ttm) cc_final: 0.6631 (mmp) REVERT: A 744 MET cc_start: 0.7392 (mtp) cc_final: 0.7079 (mtp) REVERT: A 808 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7107 (mp0) REVERT: A 825 GLU cc_start: 0.8196 (tt0) cc_final: 0.7971 (tm-30) REVERT: A 852 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7601 (mmt90) REVERT: A 920 GLU cc_start: 0.7731 (tt0) cc_final: 0.7472 (mp0) REVERT: A 981 GLU cc_start: 0.7351 (tp30) cc_final: 0.7070 (tp30) REVERT: A 1063 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: B 483 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7657 (mtp) REVERT: B 544 LEU cc_start: 0.8661 (mt) cc_final: 0.8270 (mm) REVERT: B 591 LYS cc_start: 0.8863 (mttt) cc_final: 0.8610 (mtmm) REVERT: B 603 LYS cc_start: 0.9066 (mttt) cc_final: 0.8707 (mtmp) REVERT: B 669 PHE cc_start: 0.7825 (m-80) cc_final: 0.7375 (m-80) REVERT: B 717 ARG cc_start: 0.6692 (ttt180) cc_final: 0.6212 (ttt90) REVERT: B 721 MET cc_start: 0.7045 (ttm) cc_final: 0.6615 (mmp) REVERT: B 825 GLU cc_start: 0.8194 (tt0) cc_final: 0.7968 (tm-30) REVERT: B 920 GLU cc_start: 0.7698 (tt0) cc_final: 0.7452 (mp0) REVERT: B 981 GLU cc_start: 0.7338 (tp30) cc_final: 0.7062 (tp30) REVERT: C 604 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.5750 (mtm-85) REVERT: C 606 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 669 PHE cc_start: 0.7871 (m-80) cc_final: 0.7272 (m-80) REVERT: C 808 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7066 (mp0) REVERT: C 825 GLU cc_start: 0.8123 (tt0) cc_final: 0.7863 (tm-30) REVERT: C 852 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7470 (mtt90) REVERT: C 920 GLU cc_start: 0.7670 (tt0) cc_final: 0.7445 (mp0) REVERT: C 981 GLU cc_start: 0.7430 (tp30) cc_final: 0.7082 (tm-30) REVERT: C 1063 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6490 (mp0) outliers start: 68 outliers final: 36 residues processed: 307 average time/residue: 1.3135 time to fit residues: 456.1773 Evaluate side-chains 291 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS A 855 ASN A 970 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20720 Z= 0.143 Angle : 0.486 7.433 27944 Z= 0.245 Chirality : 0.038 0.167 3212 Planarity : 0.004 0.049 3364 Dihedral : 15.623 172.131 3512 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.82 % Allowed : 19.02 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2416 helix: 1.54 (0.13), residues: 1728 sheet: 3.10 (0.81), residues: 48 loop : -0.47 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 832 HIS 0.003 0.001 HIS D 585 PHE 0.007 0.001 PHE C 612 TYR 0.007 0.001 TYR B 785 ARG 0.004 0.000 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 258 time to evaluate : 2.244 Fit side-chains REVERT: D 483 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7791 (mtm) REVERT: D 544 LEU cc_start: 0.8686 (mt) cc_final: 0.8319 (mm) REVERT: D 547 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7060 (t0) REVERT: D 591 LYS cc_start: 0.8866 (mttt) cc_final: 0.8623 (mtmm) REVERT: D 669 PHE cc_start: 0.7779 (m-80) cc_final: 0.7338 (m-80) REVERT: D 681 GLU cc_start: 0.8018 (pt0) cc_final: 0.7451 (pt0) REVERT: D 717 ARG cc_start: 0.6711 (ttt180) cc_final: 0.6272 (ttt90) REVERT: D 721 MET cc_start: 0.7014 (ttm) cc_final: 0.6621 (mmp) REVERT: D 744 MET cc_start: 0.7362 (mtp) cc_final: 0.7007 (mtp) REVERT: D 768 TYR cc_start: 0.7537 (t80) cc_final: 0.7335 (t80) REVERT: D 864 GLU cc_start: 0.7049 (tt0) cc_final: 0.6793 (tt0) REVERT: D 981 GLU cc_start: 0.7337 (tp30) cc_final: 0.7061 (tp30) REVERT: A 483 MET cc_start: 0.8033 (mtt) cc_final: 0.7711 (mmm) REVERT: A 544 LEU cc_start: 0.8645 (mt) cc_final: 0.8276 (mm) REVERT: A 591 LYS cc_start: 0.8860 (mttt) cc_final: 0.8563 (mtmm) REVERT: A 669 PHE cc_start: 0.7831 (m-80) cc_final: 0.7397 (m-80) REVERT: A 717 ARG cc_start: 0.6658 (ttt180) cc_final: 0.6147 (ttt90) REVERT: A 721 MET cc_start: 0.7009 (ttm) cc_final: 0.6642 (mmp) REVERT: A 744 MET cc_start: 0.7429 (mtp) cc_final: 0.7183 (mtp) REVERT: A 808 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7067 (mp0) REVERT: A 825 GLU cc_start: 0.8188 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 852 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7585 (mmt90) REVERT: A 920 GLU cc_start: 0.7728 (tt0) cc_final: 0.7456 (mp0) REVERT: A 981 GLU cc_start: 0.7350 (tp30) cc_final: 0.7078 (tp30) REVERT: A 1063 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: B 483 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7670 (mtp) REVERT: B 544 LEU cc_start: 0.8663 (mt) cc_final: 0.8278 (mm) REVERT: B 591 LYS cc_start: 0.8861 (mttt) cc_final: 0.8608 (mtmm) REVERT: B 603 LYS cc_start: 0.9059 (mttt) cc_final: 0.8700 (mtmp) REVERT: B 669 PHE cc_start: 0.7848 (m-80) cc_final: 0.7406 (m-80) REVERT: B 717 ARG cc_start: 0.6681 (ttt180) cc_final: 0.6213 (ttt90) REVERT: B 721 MET cc_start: 0.7022 (ttm) cc_final: 0.6605 (mmp) REVERT: B 825 GLU cc_start: 0.8184 (tt0) cc_final: 0.7962 (tm-30) REVERT: B 920 GLU cc_start: 0.7648 (tt0) cc_final: 0.7440 (mp0) REVERT: B 981 GLU cc_start: 0.7336 (tp30) cc_final: 0.7068 (tp30) REVERT: C 544 LEU cc_start: 0.8706 (mt) cc_final: 0.8297 (mm) REVERT: C 604 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.5749 (mtm-85) REVERT: C 606 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: C 669 PHE cc_start: 0.7872 (m-80) cc_final: 0.7285 (m-80) REVERT: C 808 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7020 (mp0) REVERT: C 825 GLU cc_start: 0.8139 (tt0) cc_final: 0.7885 (tm-30) REVERT: C 852 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7479 (mtt90) REVERT: C 920 GLU cc_start: 0.7634 (tt0) cc_final: 0.7433 (mp0) REVERT: C 981 GLU cc_start: 0.7444 (tp30) cc_final: 0.7055 (tm-30) REVERT: C 1063 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6472 (mp0) outliers start: 58 outliers final: 35 residues processed: 299 average time/residue: 1.3306 time to fit residues: 449.2044 Evaluate side-chains 285 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.0270 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 0.0980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 719 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS A 855 ASN A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 519 HIS ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20720 Z= 0.216 Angle : 0.520 7.618 27944 Z= 0.260 Chirality : 0.040 0.199 3212 Planarity : 0.004 0.049 3364 Dihedral : 15.530 171.605 3512 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.92 % Allowed : 19.21 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2416 helix: 1.46 (0.13), residues: 1732 sheet: 3.21 (0.82), residues: 48 loop : -0.46 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 515 HIS 0.004 0.001 HIS D 585 PHE 0.009 0.001 PHE A 583 TYR 0.009 0.001 TYR B 785 ARG 0.004 0.000 ARG B 852 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 251 time to evaluate : 2.272 Fit side-chains REVERT: D 483 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7740 (mtp) REVERT: D 544 LEU cc_start: 0.8690 (mt) cc_final: 0.8318 (mm) REVERT: D 547 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6989 (t0) REVERT: D 591 LYS cc_start: 0.8870 (mttt) cc_final: 0.8638 (mtmm) REVERT: D 669 PHE cc_start: 0.7785 (m-80) cc_final: 0.7316 (m-80) REVERT: D 681 GLU cc_start: 0.8054 (pt0) cc_final: 0.7452 (pt0) REVERT: D 717 ARG cc_start: 0.6697 (ttt180) cc_final: 0.6265 (ttt90) REVERT: D 721 MET cc_start: 0.7034 (ttm) cc_final: 0.6632 (mmp) REVERT: D 744 MET cc_start: 0.7377 (mtp) cc_final: 0.7092 (mtp) REVERT: D 864 GLU cc_start: 0.7044 (tt0) cc_final: 0.6747 (tt0) REVERT: D 981 GLU cc_start: 0.7342 (tp30) cc_final: 0.7121 (tp30) REVERT: A 483 MET cc_start: 0.8037 (mtt) cc_final: 0.7708 (mmm) REVERT: A 544 LEU cc_start: 0.8644 (mt) cc_final: 0.8273 (mm) REVERT: A 591 LYS cc_start: 0.8854 (mttt) cc_final: 0.8550 (mtmm) REVERT: A 604 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.5656 (mtm-85) REVERT: A 669 PHE cc_start: 0.7828 (m-80) cc_final: 0.7379 (m-80) REVERT: A 717 ARG cc_start: 0.6699 (ttt180) cc_final: 0.6237 (ttt90) REVERT: A 721 MET cc_start: 0.7015 (ttm) cc_final: 0.6636 (mmp) REVERT: A 744 MET cc_start: 0.7461 (mtp) cc_final: 0.7147 (mtp) REVERT: A 825 GLU cc_start: 0.8193 (tt0) cc_final: 0.7971 (tm-30) REVERT: A 920 GLU cc_start: 0.7727 (tt0) cc_final: 0.7456 (mp0) REVERT: A 981 GLU cc_start: 0.7363 (tp30) cc_final: 0.7083 (tp30) REVERT: A 1063 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: B 544 LEU cc_start: 0.8666 (mt) cc_final: 0.8268 (mm) REVERT: B 591 LYS cc_start: 0.8854 (mttt) cc_final: 0.8608 (mtmm) REVERT: B 603 LYS cc_start: 0.9077 (mttt) cc_final: 0.8715 (mtmp) REVERT: B 669 PHE cc_start: 0.7848 (m-80) cc_final: 0.7408 (m-80) REVERT: B 717 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6238 (ttt90) REVERT: B 721 MET cc_start: 0.7053 (ttm) cc_final: 0.6623 (mmp) REVERT: B 808 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7109 (mp0) REVERT: B 825 GLU cc_start: 0.8168 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 920 GLU cc_start: 0.7671 (tt0) cc_final: 0.7443 (mp0) REVERT: B 981 GLU cc_start: 0.7344 (tp30) cc_final: 0.7071 (tp30) REVERT: B 1042 MET cc_start: 0.6748 (pmm) cc_final: 0.6475 (ppp) REVERT: C 604 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.5732 (mtm-85) REVERT: C 606 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: C 669 PHE cc_start: 0.7875 (m-80) cc_final: 0.7295 (m-80) REVERT: C 825 GLU cc_start: 0.8152 (tt0) cc_final: 0.7893 (tm-30) REVERT: C 852 ARG cc_start: 0.7703 (mtt90) cc_final: 0.7459 (mtt90) REVERT: C 920 GLU cc_start: 0.7636 (tt0) cc_final: 0.7433 (mp0) REVERT: C 981 GLU cc_start: 0.7448 (tp30) cc_final: 0.7035 (tm-30) REVERT: C 1063 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6504 (mp0) outliers start: 60 outliers final: 39 residues processed: 293 average time/residue: 1.3301 time to fit residues: 439.6752 Evaluate side-chains 291 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 547 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 855 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 855 ASN Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS A 855 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20720 Z= 0.203 Angle : 0.518 8.682 27944 Z= 0.260 Chirality : 0.039 0.174 3212 Planarity : 0.004 0.049 3364 Dihedral : 15.453 172.094 3512 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 19.55 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2416 helix: 1.47 (0.13), residues: 1732 sheet: 3.25 (0.82), residues: 48 loop : -0.46 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 515 HIS 0.004 0.001 HIS D 585 PHE 0.009 0.001 PHE B 583 TYR 0.008 0.001 TYR B 785 ARG 0.004 0.000 ARG B 852 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 2.339 Fit side-chains REVERT: D 483 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7738 (mtp) REVERT: D 544 LEU cc_start: 0.8694 (mt) cc_final: 0.8317 (mm) REVERT: D 591 LYS cc_start: 0.8879 (mttt) cc_final: 0.8583 (mtmm) REVERT: D 669 PHE cc_start: 0.7783 (m-80) cc_final: 0.7304 (m-80) REVERT: D 681 GLU cc_start: 0.8037 (pt0) cc_final: 0.7450 (pt0) REVERT: D 717 ARG cc_start: 0.6698 (ttt180) cc_final: 0.6260 (ttt90) REVERT: D 721 MET cc_start: 0.7032 (ttm) cc_final: 0.6624 (mmp) REVERT: D 744 MET cc_start: 0.7383 (mtp) cc_final: 0.7046 (mtp) REVERT: D 864 GLU cc_start: 0.7018 (tt0) cc_final: 0.6773 (tt0) REVERT: D 981 GLU cc_start: 0.7329 (tp30) cc_final: 0.7116 (tp30) REVERT: A 483 MET cc_start: 0.8039 (mtt) cc_final: 0.7710 (mmm) REVERT: A 544 LEU cc_start: 0.8645 (mt) cc_final: 0.8275 (mm) REVERT: A 591 LYS cc_start: 0.8870 (mttt) cc_final: 0.8573 (mtmm) REVERT: A 669 PHE cc_start: 0.7885 (m-80) cc_final: 0.7437 (m-80) REVERT: A 717 ARG cc_start: 0.6700 (ttt180) cc_final: 0.6236 (ttt90) REVERT: A 721 MET cc_start: 0.7012 (ttm) cc_final: 0.6634 (mmp) REVERT: A 744 MET cc_start: 0.7465 (mtp) cc_final: 0.7148 (mtp) REVERT: A 825 GLU cc_start: 0.8167 (tt0) cc_final: 0.7949 (tm-30) REVERT: A 920 GLU cc_start: 0.7721 (tt0) cc_final: 0.7454 (mp0) REVERT: A 981 GLU cc_start: 0.7360 (tp30) cc_final: 0.7083 (tp30) REVERT: A 1063 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: B 544 LEU cc_start: 0.8658 (mt) cc_final: 0.8265 (mm) REVERT: B 591 LYS cc_start: 0.8853 (mttt) cc_final: 0.8609 (mtmm) REVERT: B 603 LYS cc_start: 0.9076 (mttt) cc_final: 0.8709 (mtmp) REVERT: B 669 PHE cc_start: 0.7853 (m-80) cc_final: 0.7371 (m-80) REVERT: B 717 ARG cc_start: 0.6712 (ttt180) cc_final: 0.6233 (ttt90) REVERT: B 721 MET cc_start: 0.7051 (ttm) cc_final: 0.6621 (mmp) REVERT: B 808 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7087 (mp0) REVERT: B 825 GLU cc_start: 0.8160 (tt0) cc_final: 0.7938 (tm-30) REVERT: B 920 GLU cc_start: 0.7662 (tt0) cc_final: 0.7436 (mp0) REVERT: B 981 GLU cc_start: 0.7340 (tp30) cc_final: 0.7076 (tp30) REVERT: B 1042 MET cc_start: 0.6714 (pmm) cc_final: 0.6439 (ppp) REVERT: C 604 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.5735 (mtm-85) REVERT: C 606 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: C 669 PHE cc_start: 0.7810 (m-80) cc_final: 0.7219 (m-80) REVERT: C 825 GLU cc_start: 0.8147 (tt0) cc_final: 0.7892 (tm-30) REVERT: C 852 ARG cc_start: 0.7705 (mtt90) cc_final: 0.7463 (mtt90) REVERT: C 981 GLU cc_start: 0.7448 (tp30) cc_final: 0.7042 (tm-30) REVERT: C 1063 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6507 (mp0) outliers start: 55 outliers final: 38 residues processed: 289 average time/residue: 1.3278 time to fit residues: 433.1843 Evaluate side-chains 291 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 ASP Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 606 ASP Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 483 MET Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 604 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 814 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 969 LYS Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1063 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 30.0000 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 719 HIS D 855 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS A 719 HIS A 855 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092768 restraints weight = 24916.145| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.43 r_work: 0.2801 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20720 Z= 0.238 Angle : 0.543 8.267 27944 Z= 0.272 Chirality : 0.040 0.160 3212 Planarity : 0.004 0.048 3364 Dihedral : 15.383 171.142 3512 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.82 % Allowed : 19.60 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2416 helix: 1.44 (0.13), residues: 1724 sheet: 3.28 (0.82), residues: 48 loop : -0.48 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 515 HIS 0.006 0.001 HIS D 585 PHE 0.011 0.001 PHE B 583 TYR 0.009 0.001 TYR B 785 ARG 0.004 0.001 ARG C 919 =============================================================================== Job complete usr+sys time: 7709.62 seconds wall clock time: 137 minutes 59.93 seconds (8279.93 seconds total)