Starting phenix.real_space_refine on Tue Jul 23 03:12:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/07_2024/6pqq_20451.cif" } resolution = 2.81 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= 0.003 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 28 5.49 5 S 136 5.16 5 C 13200 2.51 5 N 3148 2.21 5 O 3504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B ARG 872": "NH1" <-> "NH2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D ARG 872": "NH1" <-> "NH2" Residue "D GLU 966": "OE1" <-> "OE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C ARG 872": "NH1" <-> "NH2" Residue "C GLU 966": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 20016 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 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': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 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': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "D" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 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': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 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': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 11.19, per 1000 atoms: 0.56 Number of scatterers: 20016 At special positions: 0 Unit cell: (113.4, 113.4, 147.96, 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 136 16.00 P 28 15.00 O 3504 8.00 N 3148 7.00 C 13200 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=0, symmetry=0 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.4 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 73.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.575A pdb=" N LEU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS A 540 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 541' Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.644A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.670A pdb=" N LYS A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.341A 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 766 through 796 removed outlier: 3.765A pdb=" N PHE A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.883A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 969 Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.552A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1012 No H-bonds generated for 'chain 'A' and resid 1012 through 1012' Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 535 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS B 540 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 541 " --> pdb=" O LEU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 541' Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.645A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.669A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 740 removed outlier: 3.759A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.341A 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 766 through 796 removed outlier: 3.765A pdb=" N PHE B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.882A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.551A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1012 No H-bonds generated for 'chain 'B' and resid 1012 through 1012' Processing helix chain 'B' and resid 1016 through 1025 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'D' and resid 447 through 456 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 535 Processing helix chain 'D' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS D 540 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 537 through 541' Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.645A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.670A pdb=" N LYS D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.648A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.340A 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 766 through 796 removed outlier: 3.765A pdb=" N PHE D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.883A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 853 No H-bonds generated for 'chain 'D' and resid 851 through 853' Processing helix chain 'D' and resid 856 through 892 removed outlier: 3.730A pdb=" N ILE D 860 " --> pdb=" O CYS D 856 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.552A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP D 999 " --> pdb=" O LEU D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1012 No H-bonds generated for 'chain 'D' and resid 1012 through 1012' Processing helix chain 'D' and resid 1016 through 1025 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 456 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.622A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 535 Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.708A pdb=" N CYS C 540 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 541 " --> pdb=" O LEU C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 541' Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.644A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.669A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.340A 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 766 through 796 removed outlier: 3.765A pdb=" N PHE C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.882A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 969 Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.553A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP C 999 " --> pdb=" O LEU C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1012 No H-bonds generated for 'chain 'C' and resid 1012 through 1012' Processing helix chain 'C' and resid 1016 through 1025 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.022A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'B' and resid 745 through 746 removed outlier: 4.021A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'D' and resid 745 through 746 removed outlier: 4.022A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 746 removed outlier: 4.021A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3456 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: 6.30 Time building geometry restraints manager: 7.95 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: 3012 1.30 - 1.43: 5112 1.43 - 1.56: 11738 1.56 - 1.69: 274 1.69 - 1.81: 268 Bond restraints: 20404 Sorted by residual: bond pdb=" O2 LBN D1202 " pdb=" P1 LBN D1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" O2 LBN B1202 " pdb=" P1 LBN B1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN A1202 " pdb=" P1 LBN A1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN C1202 " pdb=" P1 LBN C1202 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O2 LBN B1201 " pdb=" P1 LBN B1201 " ideal model delta sigma weight residual 1.650 1.783 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 20399 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 460 105.81 - 112.87: 10799 112.87 - 119.94: 7418 119.94 - 127.00: 8524 127.00 - 134.06: 271 Bond angle restraints: 27472 Sorted by residual: angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.12 122.55 -14.43 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.12 122.54 -14.42 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.12 122.53 -14.41 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.12 122.52 -14.40 1.34e+00 5.57e-01 1.15e+02 angle pdb=" C ILE D 611 " pdb=" CA ILE D 611 " pdb=" CB ILE D 611 " ideal model delta sigma weight residual 111.35 105.60 5.75 1.09e+00 8.42e-01 2.79e+01 ... (remaining 27467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 11992 35.71 - 71.42: 360 71.42 - 107.12: 64 107.12 - 142.83: 28 142.83 - 178.54: 32 Dihedral angle restraints: 12476 sinusoidal: 5356 harmonic: 7120 Sorted by residual: dihedral pdb=" C19 6OU D1205 " pdb=" C20 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O22 6OU D1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU C1205 " pdb=" C20 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O22 6OU C1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A1205 " pdb=" C20 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O22 6OU A1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.53 -178.53 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3042 0.134 - 0.269: 70 0.269 - 0.403: 0 0.403 - 0.538: 8 0.538 - 0.672: 12 Chirality restraints: 3132 Sorted by residual: chirality pdb=" C20 6OU D1205 " pdb=" C19 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O30 6OU D1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU C1205 " pdb=" C19 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O30 6OU C1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU A1205 " pdb=" C19 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O30 6OU A1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 3129 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 820 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 821 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 821 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO B 821 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 821 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.038 5.00e-02 4.00e+02 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5760 2.83 - 3.35: 17625 3.35 - 3.87: 31401 3.87 - 4.38: 35950 4.38 - 4.90: 61651 Nonbonded interactions: 152387 Sorted by model distance: nonbonded pdb=" O ILE D 810 " pdb=" OG1 THR D 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE C 810 " pdb=" OG1 THR C 814 " model vdw 2.316 2.440 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.316 2.440 nonbonded pdb=" O MET B 744 " pdb=" NE1 TRP B 832 " model vdw 2.392 2.520 ... (remaining 152382 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 52.200 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.011 0.141 20404 Z= 0.687 Angle : 1.262 14.804 27472 Z= 0.561 Chirality : 0.070 0.672 3132 Planarity : 0.007 0.068 3304 Dihedral : 21.090 178.540 7844 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % 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: -3.37 (0.14), residues: 2376 helix: -2.18 (0.09), residues: 1720 sheet: -0.88 (0.68), residues: 68 loop : -1.79 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 832 HIS 0.010 0.002 HIS A 589 PHE 0.019 0.002 PHE D 888 TYR 0.033 0.003 TYR C 842 ARG 0.005 0.001 ARG D 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.9313 (mt) cc_final: 0.9078 (mp) REVERT: A 544 LEU cc_start: 0.9158 (mt) cc_final: 0.8816 (mm) REVERT: A 873 SER cc_start: 0.8434 (t) cc_final: 0.8176 (p) REVERT: A 986 LEU cc_start: 0.9074 (tt) cc_final: 0.8817 (tp) REVERT: A 992 LEU cc_start: 0.9160 (tt) cc_final: 0.8845 (tm) REVERT: B 580 GLN cc_start: 0.8506 (mp10) cc_final: 0.8119 (mp10) REVERT: B 717 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7893 (ttt90) REVERT: B 912 MET cc_start: 0.8371 (ttm) cc_final: 0.8169 (ttp) REVERT: B 1075 ILE cc_start: 0.8707 (mt) cc_final: 0.7406 (mm) REVERT: D 693 ASN cc_start: 0.8755 (m-40) cc_final: 0.8269 (t0) REVERT: D 783 PHE cc_start: 0.7805 (m-10) cc_final: 0.7510 (m-10) REVERT: D 981 GLU cc_start: 0.8049 (tp30) cc_final: 0.7848 (tp30) REVERT: D 992 LEU cc_start: 0.9092 (tt) cc_final: 0.8576 (tm) REVERT: D 1059 GLU cc_start: 0.8219 (tp30) cc_final: 0.7857 (tp30) REVERT: D 1075 ILE cc_start: 0.8795 (mt) cc_final: 0.8326 (mp) REVERT: C 475 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 634 MET cc_start: 0.8512 (tpt) cc_final: 0.7956 (tpt) REVERT: C 635 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7986 (tptp) REVERT: C 720 MET cc_start: 0.7594 (mmm) cc_final: 0.7229 (mmt) REVERT: C 854 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7761 (mp0) REVERT: C 873 SER cc_start: 0.7711 (t) cc_final: 0.7457 (p) REVERT: C 1042 MET cc_start: 0.7921 (ppp) cc_final: 0.7720 (pp-130) REVERT: C 1059 GLU cc_start: 0.8325 (tp30) cc_final: 0.7999 (tp30) outliers start: 4 outliers final: 1 residues processed: 491 average time/residue: 1.3452 time to fit residues: 739.6351 Evaluate side-chains 242 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain C residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 644 HIS A 700 HIS A 747 ASN A 805 ASN A 907 GLN A 983 HIS B 451 HIS B 476 ASN B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 805 ASN B 907 GLN B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 512 HIS D 519 HIS D 644 HIS D 700 HIS D 747 ASN D 805 ASN D 907 GLN D 983 HIS C 451 HIS C 460 ASN C 476 ASN C 512 HIS C 519 HIS C 644 HIS C 700 HIS C 747 ASN C 983 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20404 Z= 0.171 Angle : 0.580 8.080 27472 Z= 0.278 Chirality : 0.039 0.147 3132 Planarity : 0.005 0.060 3304 Dihedral : 23.692 177.016 3476 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.98 % Allowed : 14.29 % Favored : 82.74 % 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: -0.73 (0.16), residues: 2376 helix: -0.14 (0.11), residues: 1740 sheet: -0.19 (0.74), residues: 68 loop : -1.20 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 832 HIS 0.004 0.001 HIS A 451 PHE 0.012 0.001 PHE B 823 TYR 0.012 0.001 TYR A 714 ARG 0.012 0.001 ARG D 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 253 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9120 (mt) cc_final: 0.8850 (mm) REVERT: A 634 MET cc_start: 0.8518 (tpt) cc_final: 0.8259 (tpp) REVERT: A 661 LYS cc_start: 0.8824 (pttt) cc_final: 0.8594 (ptpt) REVERT: A 826 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8424 (pt) REVERT: A 877 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7764 (t80) REVERT: A 986 LEU cc_start: 0.9026 (tt) cc_final: 0.8756 (tp) REVERT: A 992 LEU cc_start: 0.9102 (tt) cc_final: 0.8657 (tm) REVERT: B 530 MET cc_start: 0.8478 (ttp) cc_final: 0.8278 (mtp) REVERT: B 580 GLN cc_start: 0.8407 (mp10) cc_final: 0.7984 (mp10) REVERT: B 826 ILE cc_start: 0.8585 (tp) cc_final: 0.8204 (pt) REVERT: B 877 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7843 (t80) REVERT: B 912 MET cc_start: 0.8503 (ttm) cc_final: 0.8244 (ttp) REVERT: B 981 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7958 (tm-30) REVERT: B 1075 ILE cc_start: 0.8737 (mt) cc_final: 0.8497 (mp) REVERT: D 634 MET cc_start: 0.8557 (tpt) cc_final: 0.8321 (tpp) REVERT: D 693 ASN cc_start: 0.8716 (m-40) cc_final: 0.8286 (t0) REVERT: D 783 PHE cc_start: 0.7810 (m-10) cc_final: 0.7549 (m-10) REVERT: D 852 ARG cc_start: 0.7724 (mmt90) cc_final: 0.7227 (mpt-90) REVERT: D 877 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7321 (t80) REVERT: D 1047 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: D 1059 GLU cc_start: 0.8217 (tp30) cc_final: 0.7853 (tp30) REVERT: C 483 MET cc_start: 0.8644 (mtm) cc_final: 0.8070 (mtp) REVERT: C 635 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7901 (tptp) REVERT: C 689 MET cc_start: 0.8442 (mtp) cc_final: 0.8092 (mtt) REVERT: C 808 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7062 (mp0) REVERT: C 873 SER cc_start: 0.7671 (t) cc_final: 0.7415 (p) REVERT: C 978 MET cc_start: 0.8198 (mtm) cc_final: 0.7954 (mtm) REVERT: C 981 GLU cc_start: 0.8135 (tp30) cc_final: 0.7912 (tp30) REVERT: C 1059 GLU cc_start: 0.8323 (tp30) cc_final: 0.7996 (tp30) outliers start: 60 outliers final: 17 residues processed: 296 average time/residue: 1.1861 time to fit residues: 399.7572 Evaluate side-chains 222 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 873 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1047 GLN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 894 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 0.0970 chunk 194 optimal weight: 7.9990 chunk 216 optimal weight: 0.0070 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 0.0060 overall best weight: 0.7614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 ASN B 570 HIS B 590 ASN B 747 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 460 ASN D 549 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 590 ASN C 692 ASN C 805 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20404 Z= 0.160 Angle : 0.536 8.142 27472 Z= 0.256 Chirality : 0.039 0.142 3132 Planarity : 0.004 0.055 3304 Dihedral : 22.102 169.620 3472 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.72 % Allowed : 14.38 % Favored : 81.89 % 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: 0.57 (0.17), residues: 2376 helix: 0.83 (0.12), residues: 1756 sheet: 0.44 (0.76), residues: 68 loop : -0.83 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 605 HIS 0.004 0.001 HIS A 494 PHE 0.009 0.001 PHE C 612 TYR 0.012 0.001 TYR C 842 ARG 0.005 0.000 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 2.287 Fit side-chains revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9138 (mt) cc_final: 0.8864 (mm) REVERT: A 826 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8465 (pt) REVERT: A 877 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7891 (t80) REVERT: A 974 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: A 986 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 530 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (mtp) REVERT: B 681 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: B 826 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8004 (pp) REVERT: B 877 PHE cc_start: 0.8228 (m-80) cc_final: 0.7929 (t80) REVERT: B 912 MET cc_start: 0.8589 (ttm) cc_final: 0.8322 (ttp) REVERT: D 483 MET cc_start: 0.9034 (mtp) cc_final: 0.8530 (mtp) REVERT: D 516 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8024 (p) REVERT: D 693 ASN cc_start: 0.8838 (m-40) cc_final: 0.8402 (t0) REVERT: D 720 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6676 (mpt) REVERT: D 744 MET cc_start: 0.7925 (mmp) cc_final: 0.7713 (mmm) REVERT: D 783 PHE cc_start: 0.7664 (m-10) cc_final: 0.7382 (m-10) REVERT: D 877 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7540 (t80) REVERT: D 1059 GLU cc_start: 0.8233 (tp30) cc_final: 0.7805 (tp30) REVERT: C 481 HIS cc_start: 0.8479 (m-70) cc_final: 0.8279 (m90) REVERT: C 483 MET cc_start: 0.8691 (mtm) cc_final: 0.8107 (mtp) REVERT: C 568 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7862 (mp) REVERT: C 634 MET cc_start: 0.8557 (tpt) cc_final: 0.8022 (tpt) REVERT: C 873 SER cc_start: 0.7761 (t) cc_final: 0.7550 (p) REVERT: C 941 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7981 (tp) REVERT: C 981 GLU cc_start: 0.8108 (tp30) cc_final: 0.7807 (tp30) REVERT: C 1059 GLU cc_start: 0.8295 (tp30) cc_final: 0.7924 (tp30) outliers start: 75 outliers final: 18 residues processed: 267 average time/residue: 1.0470 time to fit residues: 324.1405 Evaluate side-chains 219 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20404 Z= 0.147 Angle : 0.524 8.151 27472 Z= 0.249 Chirality : 0.039 0.169 3132 Planarity : 0.004 0.053 3304 Dihedral : 21.453 179.139 3472 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.12 % Allowed : 15.53 % Favored : 81.35 % 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: 1.20 (0.17), residues: 2376 helix: 1.31 (0.12), residues: 1756 sheet: 0.92 (0.76), residues: 68 loop : -0.75 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 515 HIS 0.004 0.001 HIS A 494 PHE 0.009 0.001 PHE C 823 TYR 0.012 0.001 TYR C 842 ARG 0.004 0.000 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 2.319 Fit side-chains REVERT: A 544 LEU cc_start: 0.9145 (mt) cc_final: 0.8880 (mm) REVERT: A 877 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (t80) REVERT: A 974 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7696 (tmtt) REVERT: A 986 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (tp) REVERT: A 1059 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7532 (tm-30) REVERT: B 681 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7649 (pp20) REVERT: B 808 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7767 (mm-30) REVERT: B 826 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7919 (pp) REVERT: B 881 LEU cc_start: 0.8572 (tp) cc_final: 0.8099 (tp) REVERT: B 912 MET cc_start: 0.8562 (ttm) cc_final: 0.8283 (ttp) REVERT: D 483 MET cc_start: 0.9028 (mtp) cc_final: 0.8500 (mtp) REVERT: D 516 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7947 (p) REVERT: D 693 ASN cc_start: 0.8809 (m-40) cc_final: 0.8364 (t0) REVERT: D 720 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6726 (mpt) REVERT: D 744 MET cc_start: 0.7895 (mmp) cc_final: 0.7673 (mmm) REVERT: D 783 PHE cc_start: 0.7617 (m-10) cc_final: 0.7373 (m-10) REVERT: D 852 ARG cc_start: 0.7708 (mmt90) cc_final: 0.7257 (mtp180) REVERT: D 877 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7627 (t80) REVERT: D 912 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: D 1059 GLU cc_start: 0.8241 (tp30) cc_final: 0.7856 (tp30) REVERT: C 483 MET cc_start: 0.8797 (mtm) cc_final: 0.8244 (mtp) REVERT: C 634 MET cc_start: 0.8621 (tpt) cc_final: 0.8095 (tpt) REVERT: C 719 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6429 (t-90) REVERT: C 720 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7337 (mmp) REVERT: C 744 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7664 (mmm) REVERT: C 873 SER cc_start: 0.7676 (t) cc_final: 0.7429 (p) REVERT: C 981 GLU cc_start: 0.8136 (tp30) cc_final: 0.7836 (tp30) REVERT: C 1059 GLU cc_start: 0.8278 (tp30) cc_final: 0.7883 (tp30) outliers start: 63 outliers final: 22 residues processed: 242 average time/residue: 1.0595 time to fit residues: 295.8839 Evaluate side-chains 221 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 590 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN C 979 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20404 Z= 0.166 Angle : 0.533 8.667 27472 Z= 0.251 Chirality : 0.039 0.171 3132 Planarity : 0.003 0.049 3304 Dihedral : 20.738 172.074 3472 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.72 % Allowed : 15.38 % Favored : 80.90 % 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: 1.57 (0.18), residues: 2376 helix: 1.58 (0.12), residues: 1756 sheet: 1.15 (0.77), residues: 68 loop : -0.65 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 809 HIS 0.004 0.001 HIS B 494 PHE 0.009 0.001 PHE C 823 TYR 0.009 0.001 TYR D 456 ARG 0.003 0.000 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 203 time to evaluate : 2.048 Fit side-chains REVERT: A 544 LEU cc_start: 0.9152 (mt) cc_final: 0.8881 (mm) REVERT: A 877 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7989 (t80) REVERT: A 974 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7689 (tmtt) REVERT: A 986 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8744 (tp) REVERT: A 1059 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7507 (tm-30) REVERT: B 464 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7984 (mtp180) REVERT: B 483 MET cc_start: 0.8467 (mtp) cc_final: 0.7892 (mmt) REVERT: B 681 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: B 720 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7915 (mmp) REVERT: B 808 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7778 (mm-30) REVERT: B 826 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 881 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8223 (tp) REVERT: D 483 MET cc_start: 0.9050 (mtp) cc_final: 0.8537 (mtp) REVERT: D 516 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7918 (p) REVERT: D 720 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: D 744 MET cc_start: 0.7882 (mmp) cc_final: 0.7665 (mmm) REVERT: D 852 ARG cc_start: 0.7724 (mmt90) cc_final: 0.7306 (mtp85) REVERT: D 873 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7677 (p) REVERT: D 1059 GLU cc_start: 0.8244 (tp30) cc_final: 0.7823 (tp30) REVERT: C 483 MET cc_start: 0.8797 (mtm) cc_final: 0.8172 (mtp) REVERT: C 544 LEU cc_start: 0.8930 (mt) cc_final: 0.8692 (mm) REVERT: C 634 MET cc_start: 0.8618 (tpt) cc_final: 0.8297 (tpp) REVERT: C 720 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7358 (mmp) REVERT: C 733 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7706 (tpp) REVERT: C 744 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: C 842 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.6720 (t80) REVERT: C 871 LEU cc_start: 0.8586 (mt) cc_final: 0.8093 (mp) REVERT: C 873 SER cc_start: 0.7788 (t) cc_final: 0.7515 (p) REVERT: C 981 GLU cc_start: 0.8026 (tp30) cc_final: 0.7743 (tp30) REVERT: C 1047 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6403 (mt0) REVERT: C 1059 GLU cc_start: 0.8291 (tp30) cc_final: 0.7893 (tp30) outliers start: 75 outliers final: 27 residues processed: 250 average time/residue: 1.1213 time to fit residues: 321.8158 Evaluate side-chains 231 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 0.0060 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 619 ASN A 687 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20404 Z= 0.185 Angle : 0.541 8.495 27472 Z= 0.255 Chirality : 0.040 0.156 3132 Planarity : 0.003 0.047 3304 Dihedral : 20.296 175.631 3472 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 16.62 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.18), residues: 2376 helix: 1.73 (0.12), residues: 1756 sheet: 1.26 (0.77), residues: 68 loop : -0.56 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.004 0.001 HIS D 494 PHE 0.012 0.001 PHE B 877 TYR 0.009 0.001 TYR C 456 ARG 0.007 0.001 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 193 time to evaluate : 2.037 Fit side-chains REVERT: A 544 LEU cc_start: 0.9154 (mt) cc_final: 0.8871 (mm) REVERT: A 720 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8011 (mmp) REVERT: A 842 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8715 (m-80) REVERT: A 877 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 986 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 1059 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7489 (tm-30) REVERT: B 483 MET cc_start: 0.8657 (mtp) cc_final: 0.7989 (mmt) REVERT: B 681 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: B 720 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (mmp) REVERT: B 826 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7903 (pp) REVERT: B 881 LEU cc_start: 0.8578 (tp) cc_final: 0.8242 (tp) REVERT: D 483 MET cc_start: 0.8987 (mtp) cc_final: 0.8550 (mtp) REVERT: D 516 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7905 (p) REVERT: D 530 MET cc_start: 0.8099 (mtp) cc_final: 0.7885 (mtt) REVERT: D 720 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: D 744 MET cc_start: 0.7863 (mmp) cc_final: 0.7491 (mtp) REVERT: D 852 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7390 (mtp180) REVERT: D 871 LEU cc_start: 0.8700 (tp) cc_final: 0.8481 (mm) REVERT: D 1059 GLU cc_start: 0.8243 (tp30) cc_final: 0.7816 (tp30) REVERT: C 483 MET cc_start: 0.8774 (mtm) cc_final: 0.8257 (mtp) REVERT: C 544 LEU cc_start: 0.8954 (mt) cc_final: 0.8739 (mm) REVERT: C 626 MET cc_start: 0.7843 (mtp) cc_final: 0.7385 (ttm) REVERT: C 634 MET cc_start: 0.8566 (tpt) cc_final: 0.7932 (tpt) REVERT: C 719 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6518 (t-90) REVERT: C 720 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7427 (mmp) REVERT: C 744 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7611 (mmm) REVERT: C 873 SER cc_start: 0.7843 (t) cc_final: 0.7558 (p) REVERT: C 981 GLU cc_start: 0.8019 (tp30) cc_final: 0.7715 (tp30) REVERT: C 1047 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6427 (mt0) REVERT: C 1059 GLU cc_start: 0.8287 (tp30) cc_final: 0.7854 (tp30) outliers start: 67 outliers final: 27 residues processed: 232 average time/residue: 1.1168 time to fit residues: 298.5778 Evaluate side-chains 220 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20404 Z= 0.158 Angle : 0.524 9.378 27472 Z= 0.248 Chirality : 0.039 0.200 3132 Planarity : 0.003 0.045 3304 Dihedral : 19.899 177.996 3472 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.32 % Allowed : 17.06 % Favored : 79.61 % 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: 1.94 (0.18), residues: 2376 helix: 1.84 (0.12), residues: 1756 sheet: 1.43 (0.78), residues: 68 loop : -0.50 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.004 0.001 HIS B 481 PHE 0.008 0.001 PHE B 877 TYR 0.009 0.001 TYR D 842 ARG 0.004 0.000 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 2.365 Fit side-chains REVERT: A 483 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: A 544 LEU cc_start: 0.9152 (mt) cc_final: 0.8873 (mm) REVERT: A 720 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7978 (mmp) REVERT: A 877 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 986 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 1059 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7487 (tm-30) REVERT: B 464 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: B 483 MET cc_start: 0.8514 (mtp) cc_final: 0.7906 (mmt) REVERT: B 681 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: B 720 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7939 (mmp) REVERT: B 826 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7905 (pp) REVERT: B 881 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8176 (tp) REVERT: D 483 MET cc_start: 0.8972 (mtp) cc_final: 0.8491 (mtp) REVERT: D 516 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7844 (p) REVERT: D 530 MET cc_start: 0.8104 (mtp) cc_final: 0.7875 (mtt) REVERT: D 720 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7379 (mmm) REVERT: D 721 MET cc_start: 0.7433 (mmt) cc_final: 0.7167 (mtm) REVERT: D 744 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7418 (mtp) REVERT: D 852 ARG cc_start: 0.7752 (mmt90) cc_final: 0.7350 (mtp180) REVERT: D 871 LEU cc_start: 0.8732 (tp) cc_final: 0.8476 (mt) REVERT: D 1059 GLU cc_start: 0.8228 (tp30) cc_final: 0.7794 (tp30) REVERT: C 483 MET cc_start: 0.8825 (mtm) cc_final: 0.8316 (mtp) REVERT: C 626 MET cc_start: 0.7806 (mtp) cc_final: 0.7455 (ttm) REVERT: C 634 MET cc_start: 0.8630 (tpt) cc_final: 0.8100 (tpt) REVERT: C 719 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6530 (t-90) REVERT: C 720 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7420 (mmp) REVERT: C 744 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: C 842 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.6627 (t80) REVERT: C 873 SER cc_start: 0.7835 (t) cc_final: 0.7558 (p) REVERT: C 981 GLU cc_start: 0.8038 (tp30) cc_final: 0.7710 (tp30) REVERT: C 1047 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6370 (mt0) REVERT: C 1059 GLU cc_start: 0.8311 (tp30) cc_final: 0.7878 (tp30) outliers start: 67 outliers final: 27 residues processed: 225 average time/residue: 1.1359 time to fit residues: 294.2761 Evaluate side-chains 230 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 722 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20404 Z= 0.250 Angle : 0.583 9.155 27472 Z= 0.275 Chirality : 0.041 0.187 3132 Planarity : 0.003 0.046 3304 Dihedral : 19.629 165.888 3472 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.52 % Allowed : 17.16 % Favored : 79.32 % 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: 1.85 (0.18), residues: 2376 helix: 1.76 (0.12), residues: 1756 sheet: 1.46 (0.78), residues: 68 loop : -0.49 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 515 HIS 0.005 0.001 HIS D 494 PHE 0.012 0.001 PHE D 818 TYR 0.011 0.001 TYR B 456 ARG 0.004 0.000 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 189 time to evaluate : 2.183 Fit side-chains REVERT: A 483 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8553 (mtp) REVERT: A 544 LEU cc_start: 0.9159 (mt) cc_final: 0.8858 (mm) REVERT: A 720 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8048 (mmp) REVERT: A 1059 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7466 (tm-30) REVERT: B 464 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7843 (mtp180) REVERT: B 483 MET cc_start: 0.8671 (mtp) cc_final: 0.8019 (mmt) REVERT: B 681 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: B 720 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7953 (mmp) REVERT: B 877 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7554 (t80) REVERT: B 881 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8188 (tp) REVERT: D 483 MET cc_start: 0.9012 (mtp) cc_final: 0.8511 (mtp) REVERT: D 523 MET cc_start: 0.8556 (tpp) cc_final: 0.8100 (ttp) REVERT: D 530 MET cc_start: 0.8088 (mtp) cc_final: 0.7867 (mtt) REVERT: D 720 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7249 (mmp) REVERT: D 744 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7494 (mtp) REVERT: D 852 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: D 871 LEU cc_start: 0.8718 (tp) cc_final: 0.8416 (mt) REVERT: D 1059 GLU cc_start: 0.8235 (tp30) cc_final: 0.7782 (tp30) REVERT: C 483 MET cc_start: 0.8785 (mtm) cc_final: 0.8272 (mtp) REVERT: C 488 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7581 (mm) REVERT: C 626 MET cc_start: 0.7816 (mtp) cc_final: 0.7451 (ttm) REVERT: C 744 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7577 (mmm) REVERT: C 873 SER cc_start: 0.7995 (t) cc_final: 0.7725 (p) REVERT: C 981 GLU cc_start: 0.7976 (tp30) cc_final: 0.7644 (tp30) REVERT: C 1059 GLU cc_start: 0.8335 (tp30) cc_final: 0.7831 (tp30) outliers start: 71 outliers final: 30 residues processed: 230 average time/residue: 1.1328 time to fit residues: 300.0696 Evaluate side-chains 216 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 174 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 873 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20404 Z= 0.162 Angle : 0.543 9.460 27472 Z= 0.257 Chirality : 0.039 0.251 3132 Planarity : 0.003 0.050 3304 Dihedral : 19.281 165.527 3472 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.58 % Allowed : 18.15 % Favored : 79.27 % 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: 1.98 (0.18), residues: 2376 helix: 1.88 (0.13), residues: 1756 sheet: 1.53 (0.79), residues: 68 loop : -0.51 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.003 0.001 HIS B 494 PHE 0.008 0.001 PHE A 823 TYR 0.012 0.001 TYR A 842 ARG 0.004 0.000 ARG C 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.224 Fit side-chains REVERT: A 544 LEU cc_start: 0.9151 (mt) cc_final: 0.8862 (mm) REVERT: A 720 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8050 (mmp) REVERT: A 744 MET cc_start: 0.7682 (mmp) cc_final: 0.7323 (mtm) REVERT: A 1059 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7466 (tm-30) REVERT: B 464 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7888 (mtp180) REVERT: B 483 MET cc_start: 0.8615 (mtp) cc_final: 0.8046 (mmt) REVERT: B 681 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: B 720 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7938 (mmp) REVERT: B 826 ILE cc_start: 0.8572 (tp) cc_final: 0.8148 (pp) REVERT: B 877 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7605 (t80) REVERT: B 881 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8154 (tp) REVERT: B 987 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8308 (mt-10) REVERT: D 483 MET cc_start: 0.8934 (mtp) cc_final: 0.8439 (mtp) REVERT: D 488 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7371 (mm) REVERT: D 530 MET cc_start: 0.8071 (mtp) cc_final: 0.7830 (mtt) REVERT: D 744 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7408 (mtp) REVERT: D 808 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8035 (mm-30) REVERT: D 852 ARG cc_start: 0.7767 (mmt90) cc_final: 0.7404 (mtp85) REVERT: D 871 LEU cc_start: 0.8716 (tp) cc_final: 0.8427 (mt) REVERT: D 1059 GLU cc_start: 0.8225 (tp30) cc_final: 0.7779 (tp30) REVERT: C 483 MET cc_start: 0.8820 (mtm) cc_final: 0.8321 (mtp) REVERT: C 626 MET cc_start: 0.7803 (mtp) cc_final: 0.7576 (ttm) REVERT: C 744 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7596 (mmm) REVERT: C 873 SER cc_start: 0.7845 (t) cc_final: 0.7542 (p) REVERT: C 981 GLU cc_start: 0.7999 (tp30) cc_final: 0.7664 (tp30) REVERT: C 1047 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6321 (mt0) REVERT: C 1059 GLU cc_start: 0.8278 (tp30) cc_final: 0.7823 (tp30) outliers start: 52 outliers final: 25 residues processed: 220 average time/residue: 1.1442 time to fit residues: 288.7862 Evaluate side-chains 213 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20404 Z= 0.188 Angle : 0.562 10.793 27472 Z= 0.264 Chirality : 0.040 0.230 3132 Planarity : 0.003 0.051 3304 Dihedral : 18.957 169.232 3472 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.08 % Allowed : 18.75 % Favored : 79.17 % 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: 2.00 (0.18), residues: 2376 helix: 1.89 (0.13), residues: 1756 sheet: 1.56 (0.79), residues: 68 loop : -0.48 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 515 HIS 0.004 0.001 HIS D 494 PHE 0.010 0.001 PHE A 818 TYR 0.011 0.001 TYR D1049 ARG 0.008 0.000 ARG C 872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 2.133 Fit side-chains REVERT: A 544 LEU cc_start: 0.9150 (mt) cc_final: 0.8857 (mm) REVERT: A 720 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8058 (mmp) REVERT: A 744 MET cc_start: 0.7679 (mmp) cc_final: 0.7362 (mtm) REVERT: A 1059 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7465 (tm-30) REVERT: B 464 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7853 (mtp180) REVERT: B 483 MET cc_start: 0.8647 (mtp) cc_final: 0.8017 (mmt) REVERT: B 681 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: B 720 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7953 (mmp) REVERT: B 744 MET cc_start: 0.7651 (mmp) cc_final: 0.7387 (mmm) REVERT: B 826 ILE cc_start: 0.8558 (tp) cc_final: 0.8140 (pp) REVERT: B 877 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7578 (t80) REVERT: B 881 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8178 (tp) REVERT: B 987 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: D 483 MET cc_start: 0.8963 (mtp) cc_final: 0.8464 (mtp) REVERT: D 488 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7397 (mm) REVERT: D 530 MET cc_start: 0.8095 (mtp) cc_final: 0.7845 (mtt) REVERT: D 720 MET cc_start: 0.7533 (mmm) cc_final: 0.7262 (mmp) REVERT: D 744 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7358 (mtp) REVERT: D 852 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7419 (mtp85) REVERT: D 871 LEU cc_start: 0.8737 (tp) cc_final: 0.8449 (mt) REVERT: D 912 MET cc_start: 0.8542 (ttm) cc_final: 0.8319 (ttt) REVERT: D 1059 GLU cc_start: 0.8228 (tp30) cc_final: 0.7783 (tp30) REVERT: C 483 MET cc_start: 0.8824 (mtm) cc_final: 0.8326 (mtp) REVERT: C 626 MET cc_start: 0.7890 (mtp) cc_final: 0.7625 (ttm) REVERT: C 744 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7598 (mmm) REVERT: C 808 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7750 (mm-30) REVERT: C 873 SER cc_start: 0.7890 (t) cc_final: 0.7593 (p) REVERT: C 981 GLU cc_start: 0.7987 (tp30) cc_final: 0.7668 (tp30) REVERT: C 1047 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6338 (mt0) REVERT: C 1059 GLU cc_start: 0.8339 (tp30) cc_final: 0.7840 (tp30) outliers start: 42 outliers final: 26 residues processed: 204 average time/residue: 1.1933 time to fit residues: 278.6996 Evaluate side-chains 215 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 40.0000 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086237 restraints weight = 31992.542| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.49 r_work: 0.2967 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20404 Z= 0.153 Angle : 0.542 11.355 27472 Z= 0.255 Chirality : 0.039 0.226 3132 Planarity : 0.003 0.051 3304 Dihedral : 18.563 170.113 3472 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.13 % Allowed : 18.75 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.18), residues: 2376 helix: 1.94 (0.13), residues: 1756 sheet: 1.68 (0.79), residues: 68 loop : -0.46 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.003 0.000 HIS D 494 PHE 0.009 0.001 PHE A 823 TYR 0.012 0.001 TYR D1049 ARG 0.007 0.000 ARG C 872 =============================================================================== Job complete usr+sys time: 6236.43 seconds wall clock time: 110 minutes 5.92 seconds (6605.92 seconds total)