Starting phenix.real_space_refine on Sat Feb 17 22:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/02_2024/6pqq_20451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/02_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_20451/02_2024/6pqq_20451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/02_2024/6pqq_20451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/02_2024/6pqq_20451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/02_2024/6pqq_20451_updated.pdb" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.13, per 1000 atoms: 0.51 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: 7.65 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... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 64.7% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.837A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.670A pdb=" N LYS A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 631 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 684 through 691 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 739 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 767 through 795 removed outlier: 3.765A pdb=" N PHE A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 822 Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 828 through 852 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) removed outlier: 3.710A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 5.095A 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 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.749A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) 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 992 through 998 Processing helix chain 'A' and resid 1015 through 1024 Processing helix chain 'A' and resid 1041 through 1071 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 610 removed outlier: 3.669A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 628 Processing helix chain 'B' and resid 631 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 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 739 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 767 through 795 removed outlier: 3.765A pdb=" N PHE B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 822 Proline residue: B 821 - end of helix Processing helix chain 'B' and resid 828 through 852 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) removed outlier: 3.710A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 891 removed outlier: 5.096A 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 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.748A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) 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 992 through 998 Processing helix chain 'B' and resid 1015 through 1024 Processing helix chain 'B' and resid 1041 through 1071 Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 610 removed outlier: 3.670A pdb=" N LYS D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 628 Processing helix chain 'D' and resid 631 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 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 739 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 767 through 795 removed outlier: 3.765A pdb=" N PHE D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 822 Proline residue: D 821 - end of helix Processing helix chain 'D' and resid 828 through 852 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) removed outlier: 3.709A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 5.095A 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 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.748A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 927 Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 986 removed outlier: 4.228A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) 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 992 through 998 Processing helix chain 'D' and resid 1015 through 1024 Processing helix chain 'D' and resid 1041 through 1071 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 495 through 503 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 538 through 540 No H-bonds generated for 'chain 'C' and resid 538 through 540' Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.838A pdb=" N ASN C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 610 removed outlier: 3.669A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 628 Processing helix chain 'C' and resid 631 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 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 739 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 767 through 795 removed outlier: 3.765A pdb=" N PHE C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 822 Proline residue: C 821 - end of helix Processing helix chain 'C' and resid 828 through 852 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) removed outlier: 3.710A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 5.096A 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 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.749A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 986 removed outlier: 4.227A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) 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 992 through 998 Processing helix chain 'C' and resid 1015 through 1024 Processing helix chain 'C' and resid 1041 through 1071 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= C, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'C' and resid 642 through 644 1000 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.68 Time building geometry restraints manager: 8.27 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: 5764 2.83 - 3.35: 17761 3.35 - 3.87: 31513 3.87 - 4.38: 36324 4.38 - 4.90: 61681 Nonbonded interactions: 153043 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 153038 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.770 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 51.070 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.120 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- 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= 0.674 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 : 2.401 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: 1.3527 time to fit residues: 744.9173 Evaluate side-chains 242 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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: 0.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 0.4980 chunk 217 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 644 HIS A 700 HIS 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 805 ASN 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2140 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= 0.160 Angle : 0.567 8.406 27472 Z= 0.270 Chirality : 0.039 0.149 3132 Planarity : 0.005 0.060 3304 Dihedral : 23.682 177.853 3476 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 14.63 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2376 helix: -0.28 (0.12), residues: 1724 sheet: -0.24 (0.73), residues: 68 loop : -1.11 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 832 HIS 0.003 0.001 HIS D 494 PHE 0.010 0.001 PHE B 823 TYR 0.013 0.001 TYR C 842 ARG 0.011 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 308 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.9279 (mt) cc_final: 0.9078 (mp) REVERT: A 544 LEU cc_start: 0.9116 (mt) cc_final: 0.8783 (mm) REVERT: A 661 LYS cc_start: 0.8822 (pttt) cc_final: 0.8588 (ptpt) REVERT: A 826 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 877 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 986 LEU cc_start: 0.9061 (tt) cc_final: 0.8780 (tp) REVERT: B 580 GLN cc_start: 0.8520 (mp10) cc_final: 0.8095 (mp10) REVERT: B 826 ILE cc_start: 0.8858 (tp) cc_final: 0.8527 (pt) REVERT: B 877 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7836 (t80) REVERT: B 912 MET cc_start: 0.8511 (ttm) cc_final: 0.8246 (ttp) REVERT: B 1075 ILE cc_start: 0.8733 (mt) cc_final: 0.8503 (mp) REVERT: D 783 PHE cc_start: 0.7803 (m-10) cc_final: 0.7524 (m-10) REVERT: D 852 ARG cc_start: 0.7691 (mmt90) cc_final: 0.7181 (mpt-90) REVERT: D 877 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7282 (t80) REVERT: D 912 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (ttm) REVERT: D 1047 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: D 1059 GLU cc_start: 0.8211 (tp30) cc_final: 0.7846 (tp30) REVERT: C 634 MET cc_start: 0.8560 (tpt) cc_final: 0.8053 (tpt) REVERT: C 635 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7986 (tptp) REVERT: C 689 MET cc_start: 0.8443 (mtp) cc_final: 0.8166 (mtt) REVERT: C 808 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7057 (mp0) REVERT: C 873 SER cc_start: 0.7659 (t) cc_final: 0.7411 (p) REVERT: C 981 GLU cc_start: 0.8072 (tp30) cc_final: 0.7832 (tp30) REVERT: C 1059 GLU cc_start: 0.8315 (tp30) cc_final: 0.7992 (tp30) outliers start: 52 outliers final: 17 residues processed: 291 average time/residue: 1.2171 time to fit residues: 403.0562 Evaluate side-chains 227 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 LYS 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 912 MET 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 529 THR Chi-restraints excluded: chain C residue 627 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 0.0470 chunk 194 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS A 570 HIS A 747 ASN B 460 ASN B 570 HIS B 747 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN D 570 HIS D 693 ASN D 747 ASN D 855 ASN ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS C 570 HIS C 590 ASN C 805 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20404 Z= 0.279 Angle : 0.604 8.856 27472 Z= 0.288 Chirality : 0.041 0.151 3132 Planarity : 0.004 0.056 3304 Dihedral : 22.218 168.462 3472 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.12 % Allowed : 15.18 % Favored : 80.70 % 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: 0.22 (0.17), residues: 2376 helix: 0.54 (0.12), residues: 1744 sheet: 0.24 (0.76), residues: 68 loop : -0.81 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 605 HIS 0.005 0.001 HIS D 494 PHE 0.018 0.002 PHE B 888 TYR 0.014 0.001 TYR C 706 ARG 0.007 0.001 ARG D 975 *********************** 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 292 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 209 time to evaluate : 2.373 Fit side-chains REVERT: A 544 LEU cc_start: 0.9151 (mt) cc_final: 0.8850 (mm) REVERT: A 634 MET cc_start: 0.8599 (tpt) cc_final: 0.8390 (tpt) REVERT: A 661 LYS cc_start: 0.8789 (pttt) cc_final: 0.8552 (ptpt) REVERT: A 826 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8433 (pt) REVERT: A 974 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7769 (tmtt) REVERT: A 986 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8842 (tp) REVERT: B 580 GLN cc_start: 0.8541 (mp10) cc_final: 0.8125 (mp10) REVERT: B 681 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7559 (pp20) REVERT: B 719 HIS cc_start: 0.7537 (t-170) cc_final: 0.7288 (t-170) REVERT: B 826 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8486 (pt) REVERT: B 852 ARG cc_start: 0.8219 (mpt-90) cc_final: 0.7362 (mtp180) REVERT: B 877 PHE cc_start: 0.8333 (m-80) cc_final: 0.7903 (t80) REVERT: B 912 MET cc_start: 0.8618 (ttm) cc_final: 0.8309 (ttp) REVERT: D 516 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8297 (p) REVERT: D 693 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8569 (t0) REVERT: D 720 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6727 (mpt) REVERT: D 744 MET cc_start: 0.8069 (mmp) cc_final: 0.7822 (mmm) REVERT: D 852 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7212 (mtp180) REVERT: D 873 SER cc_start: 0.7995 (t) cc_final: 0.7731 (p) REVERT: D 877 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7583 (t80) REVERT: D 912 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: C 634 MET cc_start: 0.8647 (tpt) cc_final: 0.8095 (tpt) REVERT: C 873 SER cc_start: 0.7831 (t) cc_final: 0.7581 (p) REVERT: C 941 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8170 (tp) REVERT: C 981 GLU cc_start: 0.8101 (tp30) cc_final: 0.7783 (tp30) REVERT: C 1042 MET cc_start: 0.7802 (ppp) cc_final: 0.7541 (pp-130) REVERT: C 1059 GLU cc_start: 0.8301 (tp30) cc_final: 0.7893 (tp30) outliers start: 83 outliers final: 24 residues processed: 268 average time/residue: 1.2130 time to fit residues: 372.5042 Evaluate side-chains 215 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR 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 826 ILE 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 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 779 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 873 SER Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 693 ASN 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 782 ILE 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 510 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 721 MET 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: 1.9990 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 979 GLN C1047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20404 Z= 0.154 Angle : 0.531 7.656 27472 Z= 0.253 Chirality : 0.039 0.224 3132 Planarity : 0.004 0.058 3304 Dihedral : 21.695 176.079 3472 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.08 % Allowed : 15.87 % Favored : 81.05 % 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: 0.86 (0.17), residues: 2376 helix: 1.06 (0.12), residues: 1744 sheet: 0.56 (0.75), residues: 68 loop : -0.79 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 832 HIS 0.002 0.001 HIS D 589 PHE 0.009 0.001 PHE C 823 TYR 0.009 0.001 TYR A 842 ARG 0.010 0.000 ARG A 996 *********************** 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 259 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 2.513 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7775 (mm) REVERT: A 544 LEU cc_start: 0.9140 (mt) cc_final: 0.8848 (mm) REVERT: A 634 MET cc_start: 0.8591 (tpt) cc_final: 0.8349 (tpt) REVERT: A 826 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8414 (pt) REVERT: A 974 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7678 (tmtt) REVERT: A 986 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 1059 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7518 (tm-30) REVERT: B 464 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: B 488 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 681 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: B 808 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7743 (mm-30) REVERT: B 826 ILE cc_start: 0.8886 (tp) cc_final: 0.8657 (pt) REVERT: B 877 PHE cc_start: 0.8288 (m-80) cc_final: 0.8016 (t80) REVERT: B 881 LEU cc_start: 0.8609 (tt) cc_final: 0.8089 (tp) REVERT: B 912 MET cc_start: 0.8595 (ttm) cc_final: 0.8312 (ttp) REVERT: B 1047 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6495 (mt0) REVERT: D 500 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8134 (tm) REVERT: D 516 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8190 (p) REVERT: D 664 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8686 (pm20) REVERT: D 720 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6700 (mpt) REVERT: D 744 MET cc_start: 0.7993 (mmp) cc_final: 0.7766 (mmm) REVERT: D 1059 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7558 (tp30) REVERT: C 634 MET cc_start: 0.8662 (tpt) cc_final: 0.8050 (tpt) REVERT: C 720 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7041 (mpt) REVERT: C 873 SER cc_start: 0.7760 (t) cc_final: 0.7495 (p) REVERT: C 981 GLU cc_start: 0.8068 (tp30) cc_final: 0.7751 (tp30) REVERT: C 1059 GLU cc_start: 0.8226 (tp30) cc_final: 0.7834 (tp30) outliers start: 62 outliers final: 22 residues processed: 238 average time/residue: 1.2097 time to fit residues: 327.5307 Evaluate side-chains 211 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 635 LYS 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 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 995 LEU Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 664 GLN 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 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 720 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** D 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN C1047 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20404 Z= 0.174 Angle : 0.532 8.882 27472 Z= 0.252 Chirality : 0.039 0.152 3132 Planarity : 0.004 0.051 3304 Dihedral : 20.947 165.261 3472 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.62 % Allowed : 15.92 % Favored : 80.46 % 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: 1.28 (0.18), residues: 2376 helix: 1.37 (0.13), residues: 1740 sheet: 0.95 (0.76), residues: 68 loop : -0.66 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.003 0.001 HIS D 494 PHE 0.009 0.001 PHE C 823 TYR 0.009 0.001 TYR A 842 ARG 0.006 0.000 ARG A 996 *********************** 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 261 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 188 time to evaluate : 2.347 Fit side-chains REVERT: A 488 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7751 (mm) REVERT: A 544 LEU cc_start: 0.9141 (mt) cc_final: 0.8843 (mm) REVERT: A 723 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 826 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8397 (pt) REVERT: A 842 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: A 974 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7670 (tmtt) REVERT: A 986 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8792 (tp) REVERT: A 1059 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7505 (tm-30) REVERT: B 464 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8009 (mtp180) REVERT: B 483 MET cc_start: 0.8633 (mtp) cc_final: 0.7901 (mmt) REVERT: B 488 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7921 (mm) REVERT: B 681 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: B 720 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7888 (mmp) REVERT: B 826 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8566 (pt) REVERT: B 877 PHE cc_start: 0.8277 (m-80) cc_final: 0.8022 (t80) REVERT: B 881 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 912 MET cc_start: 0.8563 (ttm) cc_final: 0.8318 (ttp) REVERT: B 1047 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6551 (mt0) REVERT: D 488 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7492 (mm) REVERT: D 500 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (tm) REVERT: D 516 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8106 (p) REVERT: D 663 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8169 (mt) REVERT: D 664 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: D 693 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8575 (m-40) REVERT: D 720 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6778 (mpt) REVERT: D 744 MET cc_start: 0.7989 (mmp) cc_final: 0.7761 (mmm) REVERT: D 852 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7359 (mtp85) REVERT: D 1059 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7517 (tp30) REVERT: C 544 LEU cc_start: 0.8939 (mt) cc_final: 0.8719 (mm) REVERT: C 634 MET cc_start: 0.8821 (tpt) cc_final: 0.8245 (tpt) REVERT: C 719 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6550 (t-90) REVERT: C 744 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: C 873 SER cc_start: 0.7775 (t) cc_final: 0.7490 (p) REVERT: C 981 GLU cc_start: 0.8036 (tp30) cc_final: 0.7726 (tp30) REVERT: C 1047 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6582 (mt0) REVERT: C 1059 GLU cc_start: 0.8292 (tp30) cc_final: 0.7869 (tp30) outliers start: 73 outliers final: 24 residues processed: 235 average time/residue: 1.1841 time to fit residues: 319.0518 Evaluate side-chains 222 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 174 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 635 LYS 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 723 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 842 TYR 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 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 B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 693 ASN 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 529 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 208 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 722 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN D 907 GLN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20404 Z= 0.305 Angle : 0.600 9.467 27472 Z= 0.285 Chirality : 0.042 0.186 3132 Planarity : 0.004 0.049 3304 Dihedral : 20.605 165.533 3472 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.57 % Allowed : 16.57 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.18), residues: 2376 helix: 1.36 (0.13), residues: 1744 sheet: 1.03 (0.77), residues: 68 loop : -0.57 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 515 HIS 0.005 0.001 HIS C 494 PHE 0.016 0.002 PHE C 846 TYR 0.012 0.001 TYR C 706 ARG 0.014 0.001 ARG A 996 *********************** 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 251 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 179 time to evaluate : 2.387 Fit side-chains revert: symmetry clash REVERT: A 488 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 544 LEU cc_start: 0.9155 (mt) cc_final: 0.8825 (mm) REVERT: A 1059 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7498 (tm-30) REVERT: B 464 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: B 488 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8004 (mm) REVERT: B 681 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: B 877 PHE cc_start: 0.8320 (m-80) cc_final: 0.7960 (t80) REVERT: B 881 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 912 MET cc_start: 0.8638 (ttm) cc_final: 0.8348 (ttp) REVERT: B 1047 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6492 (mt0) REVERT: D 488 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7421 (mm) REVERT: D 500 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8124 (tm) REVERT: D 663 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (mt) REVERT: D 664 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: D 720 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6813 (mpt) REVERT: D 744 MET cc_start: 0.8005 (mmp) cc_final: 0.7770 (mmm) REVERT: D 1059 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7556 (tp30) REVERT: C 495 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (p0) REVERT: C 544 LEU cc_start: 0.8970 (mt) cc_final: 0.8764 (mm) REVERT: C 744 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7588 (mmm) REVERT: C 873 SER cc_start: 0.7924 (t) cc_final: 0.7643 (p) REVERT: C 981 GLU cc_start: 0.8019 (tp30) cc_final: 0.7671 (tp30) REVERT: C 1059 GLU cc_start: 0.8310 (tp30) cc_final: 0.7808 (tp30) outliers start: 72 outliers final: 28 residues processed: 224 average time/residue: 1.1774 time to fit residues: 302.3054 Evaluate side-chains 208 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 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 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 709 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 GLN 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 529 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20404 Z= 0.206 Angle : 0.558 9.851 27472 Z= 0.264 Chirality : 0.040 0.226 3132 Planarity : 0.004 0.050 3304 Dihedral : 20.247 167.205 3472 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.42 % Allowed : 16.82 % Favored : 79.76 % 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: 1.50 (0.18), residues: 2376 helix: 1.53 (0.13), residues: 1744 sheet: 1.13 (0.77), residues: 68 loop : -0.61 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.003 0.001 HIS D 494 PHE 0.009 0.001 PHE A 583 TYR 0.010 0.001 TYR D 842 ARG 0.006 0.000 ARG A 996 *********************** 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: 69 poor density : 185 time to evaluate : 2.422 Fit side-chains REVERT: A 488 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7750 (mm) REVERT: A 530 MET cc_start: 0.8368 (mtp) cc_final: 0.8167 (mtp) REVERT: A 544 LEU cc_start: 0.9149 (mt) cc_final: 0.8833 (mm) REVERT: A 720 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (mmp) REVERT: A 826 ILE cc_start: 0.8698 (tp) cc_final: 0.8261 (pt) REVERT: A 1059 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7479 (tm-30) REVERT: B 464 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7993 (mtp180) REVERT: B 483 MET cc_start: 0.8672 (mtp) cc_final: 0.7891 (mmt) REVERT: B 488 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7979 (mm) REVERT: B 681 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7476 (pp20) REVERT: B 720 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7916 (mmp) REVERT: B 877 PHE cc_start: 0.8309 (m-80) cc_final: 0.8035 (t80) REVERT: B 881 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 912 MET cc_start: 0.8556 (ttm) cc_final: 0.8322 (ttp) REVERT: B 1047 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6621 (mt0) REVERT: D 488 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7435 (mm) REVERT: D 500 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (tm) REVERT: D 634 MET cc_start: 0.8697 (tpt) cc_final: 0.8383 (tpp) REVERT: D 664 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: D 720 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6778 (mpt) REVERT: D 744 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7770 (mmm) REVERT: D 852 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7474 (mtp85) REVERT: D 953 MET cc_start: 0.8175 (mmt) cc_final: 0.7953 (mmp) REVERT: D 1059 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 475 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7926 (tp) REVERT: C 744 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: C 785 TYR cc_start: 0.7665 (m-10) cc_final: 0.7453 (m-10) REVERT: C 873 SER cc_start: 0.7867 (t) cc_final: 0.7582 (p) REVERT: C 981 GLU cc_start: 0.8009 (tp30) cc_final: 0.7657 (tp30) REVERT: C 1059 GLU cc_start: 0.8282 (tp30) cc_final: 0.7791 (tp30) outliers start: 69 outliers final: 27 residues processed: 229 average time/residue: 1.2058 time to fit residues: 315.7663 Evaluate side-chains 218 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 2.202 ------------------------------------------------------------------------------- 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 635 LYS 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 B residue 464 ARG 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 709 MET 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 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 664 GLN 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 510 SER 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 782 ILE Chi-restraints excluded: chain C residue 941 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C1047 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20404 Z= 0.249 Angle : 0.573 9.839 27472 Z= 0.271 Chirality : 0.041 0.182 3132 Planarity : 0.004 0.045 3304 Dihedral : 19.990 173.762 3472 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.32 % Allowed : 17.16 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2376 helix: 1.54 (0.13), residues: 1748 sheet: 1.15 (0.77), residues: 68 loop : -0.54 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.004 0.001 HIS C 494 PHE 0.011 0.001 PHE C 846 TYR 0.009 0.001 TYR A 706 ARG 0.007 0.000 ARG A 996 *********************** 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 242 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 175 time to evaluate : 2.362 Fit side-chains REVERT: A 488 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7716 (mm) REVERT: A 544 LEU cc_start: 0.9153 (mt) cc_final: 0.8817 (mm) REVERT: A 720 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8022 (mmp) REVERT: A 1059 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7479 (tm-30) REVERT: B 464 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7975 (mtp180) REVERT: B 483 MET cc_start: 0.8724 (mtp) cc_final: 0.7999 (mmt) REVERT: B 488 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7998 (mm) REVERT: B 681 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: B 720 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7941 (mmp) REVERT: B 877 PHE cc_start: 0.8307 (m-80) cc_final: 0.7954 (t80) REVERT: B 881 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8212 (tp) REVERT: B 912 MET cc_start: 0.8593 (ttm) cc_final: 0.8370 (ttp) REVERT: B 1047 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6537 (mt0) REVERT: D 488 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7489 (mm) REVERT: D 500 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8117 (tm) REVERT: D 634 MET cc_start: 0.8710 (tpt) cc_final: 0.8404 (tpp) REVERT: D 663 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8124 (mt) REVERT: D 664 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: D 720 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6819 (mpt) REVERT: D 744 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7525 (mtp) REVERT: D 852 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7484 (mtp85) REVERT: D 871 LEU cc_start: 0.8736 (tp) cc_final: 0.8373 (mt) REVERT: D 981 GLU cc_start: 0.8181 (tp30) cc_final: 0.7928 (tp30) REVERT: D 1059 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7565 (tp30) REVERT: C 744 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7571 (mmm) REVERT: C 785 TYR cc_start: 0.7827 (m-10) cc_final: 0.7623 (m-10) REVERT: C 873 SER cc_start: 0.7902 (t) cc_final: 0.7622 (p) REVERT: C 981 GLU cc_start: 0.8011 (tp30) cc_final: 0.7651 (tp30) REVERT: C 1059 GLU cc_start: 0.8331 (tp30) cc_final: 0.7820 (tp30) outliers start: 67 outliers final: 34 residues processed: 218 average time/residue: 1.2854 time to fit residues: 319.3570 Evaluate side-chains 223 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 871 LEU Chi-restraints excluded: chain A residue 941 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 709 MET 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 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 741 LYS 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1043 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 510 SER 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 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 964 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.0970 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 0.0770 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20404 Z= 0.153 Angle : 0.531 9.807 27472 Z= 0.251 Chirality : 0.039 0.213 3132 Planarity : 0.003 0.048 3304 Dihedral : 19.654 174.729 3472 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.73 % Allowed : 17.81 % Favored : 79.46 % 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: 1.72 (0.18), residues: 2376 helix: 1.70 (0.13), residues: 1748 sheet: 1.22 (0.77), residues: 68 loop : -0.57 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 832 HIS 0.002 0.000 HIS D 494 PHE 0.008 0.001 PHE A 823 TYR 0.010 0.001 TYR D 842 ARG 0.006 0.000 ARG A 996 *********************** 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 240 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 185 time to evaluate : 2.314 Fit side-chains REVERT: A 488 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7812 (mm) REVERT: A 544 LEU cc_start: 0.9160 (mt) cc_final: 0.8842 (mm) REVERT: A 720 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8016 (mmp) REVERT: A 826 ILE cc_start: 0.8792 (tp) cc_final: 0.8497 (pt) REVERT: A 1059 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7462 (tm-30) REVERT: B 464 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7921 (mtp180) REVERT: B 483 MET cc_start: 0.8621 (mtp) cc_final: 0.8020 (mmt) REVERT: B 681 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7447 (pp20) REVERT: B 720 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7929 (mmp) REVERT: B 877 PHE cc_start: 0.8280 (m-80) cc_final: 0.8033 (t80) REVERT: B 881 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 911 MET cc_start: 0.8607 (mtm) cc_final: 0.8388 (mtp) REVERT: B 1047 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: D 500 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8126 (tm) REVERT: D 663 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8159 (mt) REVERT: D 664 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: D 744 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7502 (mtp) REVERT: D 808 GLU cc_start: 0.8212 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 852 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7489 (mtp85) REVERT: D 871 LEU cc_start: 0.8734 (tp) cc_final: 0.8359 (mt) REVERT: D 912 MET cc_start: 0.8508 (ttm) cc_final: 0.8295 (ttt) REVERT: D 981 GLU cc_start: 0.8226 (tp30) cc_final: 0.7949 (tp30) REVERT: D 1059 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7523 (tp30) REVERT: C 475 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7979 (tp) REVERT: C 744 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: C 785 TYR cc_start: 0.7701 (m-10) cc_final: 0.7388 (m-10) REVERT: C 873 SER cc_start: 0.7827 (t) cc_final: 0.7529 (p) REVERT: C 981 GLU cc_start: 0.8011 (tp30) cc_final: 0.7648 (tp30) REVERT: C 1047 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6657 (mt0) REVERT: C 1059 GLU cc_start: 0.8328 (tp30) cc_final: 0.7857 (tp30) outliers start: 55 outliers final: 26 residues processed: 215 average time/residue: 1.2557 time to fit residues: 308.1819 Evaluate side-chains 214 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 635 LYS 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 998 VAL Chi-restraints excluded: chain B residue 464 ARG 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 709 MET 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 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 709 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 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 720 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 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: 0.7811 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20404 Z= 0.162 Angle : 0.538 10.801 27472 Z= 0.254 Chirality : 0.039 0.211 3132 Planarity : 0.003 0.046 3304 Dihedral : 19.313 178.400 3472 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 18.40 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 2376 helix: 1.76 (0.13), residues: 1744 sheet: 1.29 (0.78), residues: 68 loop : -0.53 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.002 0.001 HIS D 494 PHE 0.007 0.001 PHE C 823 TYR 0.010 0.001 TYR D 842 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 231 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 183 time to evaluate : 2.213 Fit side-chains REVERT: A 488 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7811 (mm) REVERT: A 544 LEU cc_start: 0.9157 (mt) cc_final: 0.8838 (mm) REVERT: A 720 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8050 (mmp) REVERT: A 744 MET cc_start: 0.7803 (mmp) cc_final: 0.7431 (mtm) REVERT: A 826 ILE cc_start: 0.8765 (tp) cc_final: 0.8429 (pt) REVERT: A 1059 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7439 (tm-30) REVERT: B 464 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7919 (mtp180) REVERT: B 483 MET cc_start: 0.8639 (mtp) cc_final: 0.8002 (mmt) REVERT: B 681 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: B 720 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7966 (mmp) REVERT: B 852 ARG cc_start: 0.8227 (mpt-90) cc_final: 0.7525 (mtp180) REVERT: B 881 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8217 (tp) REVERT: B 912 MET cc_start: 0.8546 (ttp) cc_final: 0.8293 (ttp) REVERT: B 1047 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6749 (mt0) REVERT: B 1073 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: D 500 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8182 (tm) REVERT: D 634 MET cc_start: 0.8719 (tpt) cc_final: 0.8434 (tpp) REVERT: D 663 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8103 (mt) REVERT: D 664 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8593 (pm20) REVERT: D 720 MET cc_start: 0.7509 (mmm) cc_final: 0.7241 (mmp) REVERT: D 744 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7504 (mtp) REVERT: D 852 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7497 (mtp85) REVERT: D 871 LEU cc_start: 0.8743 (tp) cc_final: 0.8391 (mt) REVERT: D 981 GLU cc_start: 0.8210 (tp30) cc_final: 0.7930 (tp30) REVERT: D 1059 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7477 (tp30) REVERT: C 475 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 744 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7576 (mmm) REVERT: C 785 TYR cc_start: 0.7776 (m-10) cc_final: 0.7476 (m-10) REVERT: C 873 SER cc_start: 0.7817 (t) cc_final: 0.7510 (p) REVERT: C 981 GLU cc_start: 0.8043 (tp30) cc_final: 0.7681 (tp30) REVERT: C 1059 GLU cc_start: 0.8326 (tp30) cc_final: 0.7850 (tp30) outliers start: 48 outliers final: 25 residues processed: 209 average time/residue: 1.2629 time to fit residues: 301.3196 Evaluate side-chains 219 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 871 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG 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 709 MET 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 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 GLN Chi-restraints excluded: chain D residue 709 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 852 ARG Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 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 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084652 restraints weight = 32098.724| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.55 r_work: 0.2919 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20404 Z= 0.165 Angle : 0.536 11.107 27472 Z= 0.254 Chirality : 0.039 0.205 3132 Planarity : 0.003 0.048 3304 Dihedral : 18.845 175.726 3472 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.38 % Allowed : 18.30 % 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: 1.77 (0.13), residues: 1748 sheet: 1.33 (0.78), residues: 68 loop : -0.46 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.002 0.001 HIS D 494 PHE 0.009 0.001 PHE D 877 TYR 0.010 0.001 TYR D1049 ARG 0.008 0.000 ARG C 872 =============================================================================== Job complete usr+sys time: 6427.87 seconds wall clock time: 115 minutes 25.40 seconds (6925.40 seconds total)