Starting phenix.real_space_refine on Sat Feb 17 15:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ssb_40750/02_2024/8ssb_40750_updated.pdb" } resolution = 3.66 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 18 5.49 5 S 132 5.16 5 C 12575 2.51 5 N 2907 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D ARG 819": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "B GLU 1104": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 585} Chain breaks: 4 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 394} Chain breaks: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 250 Unusual residues: {'PCW': 8} Inner-chain residues flagged as termini: ['pdbres="GLU A1108 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'PCW': 4, 'SPD': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B1104 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 199 Unusual residues: {'PCW': 7} Inner-chain residues flagged as termini: ['pdbres="GLU C1107 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PCW:plan-1': 4, 'PCW:plan-2': 1, 'PCW:plan-3': 4, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 174 Unusual residues: {'PCW': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'PCW': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 12.27, per 1000 atoms: 0.64 Number of scatterers: 19048 At special positions: 0 Unit cell: (117.86, 122.01, 134.46, 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 132 16.00 P 18 15.00 O 3416 8.00 N 2907 7.00 C 12575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.02 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.02 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.02 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 7.40 Conformation dependent library (CDL) restraints added in 3.6 seconds 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 6 sheets defined 52.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 removed outlier: 3.520A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.649A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 483 through 488' Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.119A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.720A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.722A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 667 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 4.167A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.521A pdb=" N VAL A 746 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 765 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 794 through 821 removed outlier: 3.824A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 857 removed outlier: 3.597A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 950 Proline residue: A 930 - end of helix removed outlier: 3.909A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 3.711A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1031 removed outlier: 3.861A pdb=" N ILE A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A1013 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 Processing helix chain 'B' and resid 417 through 420 removed outlier: 3.504A pdb=" N ARG B 420 " --> pdb=" O GLY B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.583A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.528A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 removed outlier: 4.444A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 525 through 545 removed outlier: 4.135A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 584 removed outlier: 3.562A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 removed outlier: 4.116A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.682A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.558A pdb=" N VAL B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.859A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 756 removed outlier: 4.122A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 4.245A pdb=" N LEU B 748 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 751 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 755 " --> pdb=" O LYS B 752 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN B 756 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 793 through 818 removed outlier: 3.578A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.519A pdb=" N ARG C 420 " --> pdb=" O GLY C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.649A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 483 through 488' Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 543 removed outlier: 4.119A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 598 through 627 removed outlier: 3.720A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 removed outlier: 3.722A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 667 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 4.166A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.521A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 765 Processing helix chain 'C' and resid 778 through 780 No H-bonds generated for 'chain 'C' and resid 778 through 780' Processing helix chain 'C' and resid 794 through 821 removed outlier: 3.824A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 857 removed outlier: 3.596A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 950 Proline residue: C 930 - end of helix removed outlier: 3.909A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 3.712A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1031 removed outlier: 3.861A pdb=" N ILE C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1013 " --> pdb=" O PHE C1009 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 Processing helix chain 'D' and resid 417 through 420 removed outlier: 3.504A pdb=" N ARG D 420 " --> pdb=" O GLY D 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 424 through 433 removed outlier: 3.583A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 467 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.529A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 520 removed outlier: 4.444A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 525 through 545 removed outlier: 4.135A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 539 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 584 removed outlier: 3.562A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 623 removed outlier: 4.116A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 660 removed outlier: 3.683A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.559A pdb=" N VAL D 690 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.859A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 756 removed outlier: 4.122A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 4.245A pdb=" N LEU D 748 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 751 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU D 755 " --> pdb=" O LYS D 752 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN D 756 " --> pdb=" O LEU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 818 removed outlier: 3.577A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 23 removed outlier: 3.585A pdb=" N THR E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.616A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 removed outlier: 4.183A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 4.442A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 106 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 127 through 157 removed outlier: 3.574A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 23 removed outlier: 3.518A pdb=" N THR F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 removed outlier: 3.653A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 Processing helix chain 'F' and resid 66 through 85 removed outlier: 4.322A pdb=" N VAL F 69 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 3.737A pdb=" N SER F 73 " --> pdb=" O PRO F 70 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE F 78 " --> pdb=" O HIS F 75 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS F 79 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 83 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 127 through 157 removed outlier: 3.662A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 396 through 399 removed outlier: 5.978A pdb=" N LYS A 441 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A 399 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR A 443 " --> pdb=" O THR A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 503 through 505 removed outlier: 3.647A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 502 through 505 removed outlier: 4.044A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 396 through 399 removed outlier: 5.978A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 503 through 505 removed outlier: 3.647A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 502 through 505 removed outlier: 4.044A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 699 hydrogen bonds defined for protein. 2028 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: 5.02 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2884 1.31 - 1.44: 5292 1.44 - 1.57: 11003 1.57 - 1.69: 36 1.69 - 1.82: 212 Bond restraints: 19427 Sorted by residual: bond pdb=" C ASP C 519 " pdb=" N PRO C 520 " ideal model delta sigma weight residual 1.336 1.386 -0.051 1.08e-02 8.57e+03 2.20e+01 bond pdb=" C ASP A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.336 1.386 -0.050 1.08e-02 8.57e+03 2.15e+01 bond pdb=" C31 PCW C1102 " pdb=" O2 PCW C1102 " ideal model delta sigma weight residual 1.333 1.424 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C VAL F 69 " pdb=" N PRO F 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C VAL E 69 " pdb=" N PRO E 70 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.30e-02 5.92e+03 2.03e+01 ... (remaining 19422 not shown) Histogram of bond angle deviations from ideal: 95.87 - 104.15: 228 104.15 - 112.42: 9622 112.42 - 120.70: 9981 120.70 - 128.98: 6059 128.98 - 137.26: 170 Bond angle restraints: 26060 Sorted by residual: angle pdb=" C ASN A 411 " pdb=" N HIS A 412 " pdb=" CA HIS A 412 " ideal model delta sigma weight residual 121.54 134.09 -12.55 1.91e+00 2.74e-01 4.32e+01 angle pdb=" C ASN C 411 " pdb=" N HIS C 412 " pdb=" CA HIS C 412 " ideal model delta sigma weight residual 121.54 134.05 -12.51 1.91e+00 2.74e-01 4.29e+01 angle pdb=" C ASP C 454 " pdb=" N ALA C 455 " pdb=" CA ALA C 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ASP A 454 " pdb=" N ALA A 455 " pdb=" CA ALA A 455 " ideal model delta sigma weight residual 120.79 129.69 -8.90 1.39e+00 5.18e-01 4.10e+01 angle pdb=" C ILE C 591 " pdb=" N SER C 592 " pdb=" CA SER C 592 " ideal model delta sigma weight residual 121.80 137.26 -15.46 2.44e+00 1.68e-01 4.01e+01 ... (remaining 26055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 11207 35.54 - 71.09: 379 71.09 - 106.63: 37 106.63 - 142.17: 8 142.17 - 177.72: 2 Dihedral angle restraints: 11633 sinusoidal: 4991 harmonic: 6642 Sorted by residual: dihedral pdb=" CA SER A 403 " pdb=" C SER A 403 " pdb=" N PRO A 404 " pdb=" CA PRO A 404 " ideal model delta harmonic sigma weight residual 180.00 -119.87 -60.13 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA SER C 403 " pdb=" C SER C 403 " pdb=" N PRO C 404 " pdb=" CA PRO C 404 " ideal model delta harmonic sigma weight residual 180.00 -119.88 -60.12 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LYS C 458 " pdb=" C LYS C 458 " pdb=" N ILE C 459 " pdb=" CA ILE C 459 " ideal model delta harmonic sigma weight residual -180.00 -125.97 -54.03 0 5.00e+00 4.00e-02 1.17e+02 ... (remaining 11630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2198 0.064 - 0.128: 522 0.128 - 0.192: 88 0.192 - 0.256: 20 0.256 - 0.320: 8 Chirality restraints: 2836 Sorted by residual: chirality pdb=" C2 PCW B1101 " pdb=" C1 PCW B1101 " pdb=" C3 PCW B1101 " pdb=" O2 PCW B1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE D 459 " pdb=" CA ILE D 459 " pdb=" CG1 ILE D 459 " pdb=" CG2 ILE D 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE B 459 " pdb=" CA ILE B 459 " pdb=" CG1 ILE B 459 " pdb=" CG2 ILE B 459 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2833 not shown) Planarity restraints: 3142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO B 717 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " 0.067 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO D 717 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 403 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.57e+00 pdb=" N PRO A 404 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " 0.042 5.00e-02 4.00e+02 ... (remaining 3139 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4733 2.79 - 3.31: 17755 3.31 - 3.84: 31819 3.84 - 4.37: 37528 4.37 - 4.90: 60680 Nonbonded interactions: 152515 Sorted by model distance: nonbonded pdb=" OG SER A 729 " pdb=" OG SER D 729 " model vdw 2.258 2.440 nonbonded pdb=" O ASP B 490 " pdb=" OG1 THR B 736 " model vdw 2.268 2.440 nonbonded pdb=" O ASP D 490 " pdb=" OG1 THR D 736 " model vdw 2.268 2.440 nonbonded pdb=" OE1 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.278 2.440 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.278 2.440 ... (remaining 152510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 1035 or resid 1101 or (resid 1102 through 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C5 or name C6 or name C7 or name C8 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or (resid 1104 through 1106 and (name C13 or name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23)) or resid 1108 through 1109)) selection = (chain 'C' and (resid 394 through 1035 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C20 or na \ me C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C42 \ or name C43 or name C44 or name C45 or name C5 or name C6 or name C7 or name C8 \ or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O \ 3P or name O4P or name P )) or resid 1104 through 1108)) } ncs_group { reference = (chain 'B' and (resid 394 through 821 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or \ name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or \ name O31 or name O3P or name O4P or name P )) or (resid 1105 and (name N or nam \ e C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C41 or nam \ e C5 or name C6 or name C7 or name C8 or name O11 or name O1P or name O2 or name \ O2P or name O3 or name O31 or name O3P or name O4P or name P )))) selection = (chain 'D' and (resid 394 through 821 or resid 1101 through 1102 or (resid 1103 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or name C6 or \ name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 or \ name O31 or name O3P or name O4P or name P )) or resid 1104)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) selection = (chain 'F' and (resid 2 through 159 or (resid 202 and (name C13 or name C14 or n \ ame C15 or name C16 or name C17 or name C18 or name C19 or name C20)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 19.550 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 52.290 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.009 0.094 19427 Z= 0.587 Angle : 1.545 15.457 26060 Z= 0.805 Chirality : 0.060 0.320 2836 Planarity : 0.008 0.101 3142 Dihedral : 17.483 177.715 7367 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.40 % Favored : 87.37 % Rotamer: Outliers : 0.72 % Allowed : 6.49 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 9.38 % Twisted General : 1.35 % 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: -5.92 (0.12), residues: 2264 helix: -3.81 (0.08), residues: 1320 sheet: -4.58 (0.35), residues: 102 loop : -3.75 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 578 HIS 0.013 0.003 HIS E 27 PHE 0.026 0.003 PHE A 546 TYR 0.033 0.003 TYR F 149 ARG 0.007 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 650 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.9021 (ttp) cc_final: 0.8633 (ttm) REVERT: A 467 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 585 MET cc_start: 0.8384 (mpt) cc_final: 0.7829 (mpt) REVERT: A 657 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 713 GLU cc_start: 0.8629 (pp20) cc_final: 0.8380 (pp20) REVERT: A 879 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8098 (mmtm) REVERT: A 938 PHE cc_start: 0.8754 (m-10) cc_final: 0.8501 (m-80) REVERT: A 943 PHE cc_start: 0.9008 (t80) cc_final: 0.8570 (t80) REVERT: A 968 LEU cc_start: 0.8985 (mt) cc_final: 0.8766 (mt) REVERT: A 1003 TYR cc_start: 0.8063 (m-80) cc_final: 0.7341 (m-80) REVERT: A 1005 TRP cc_start: 0.5466 (m100) cc_final: 0.5156 (m-90) REVERT: A 1028 PHE cc_start: 0.8162 (t80) cc_final: 0.7945 (t80) REVERT: A 1029 MET cc_start: 0.7793 (mmm) cc_final: 0.7506 (mtt) REVERT: B 421 TYR cc_start: 0.7901 (m-10) cc_final: 0.7632 (m-10) REVERT: B 460 TRP cc_start: 0.6636 (m-90) cc_final: 0.6428 (m-10) REVERT: B 626 VAL cc_start: 0.9301 (t) cc_final: 0.9038 (m) REVERT: B 713 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8626 (tm-30) REVERT: B 714 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7256 (tp40) REVERT: B 760 ASP cc_start: 0.9255 (m-30) cc_final: 0.8811 (t70) REVERT: B 761 LYS cc_start: 0.9498 (tptp) cc_final: 0.9238 (tppt) REVERT: B 764 ASN cc_start: 0.8725 (m-40) cc_final: 0.8189 (m110) REVERT: C 461 ASN cc_start: 0.8081 (t0) cc_final: 0.7807 (p0) REVERT: C 463 MET cc_start: 0.9121 (ttp) cc_final: 0.8853 (ttm) REVERT: C 657 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7726 (mm-30) REVERT: C 695 LYS cc_start: 0.9067 (mttp) cc_final: 0.8638 (mmtt) REVERT: C 714 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8330 (mm-40) REVERT: C 879 LYS cc_start: 0.8123 (ttpt) cc_final: 0.7410 (mmtm) REVERT: C 926 ARG cc_start: 0.6446 (ttm-80) cc_final: 0.5923 (ttt90) REVERT: C 1029 MET cc_start: 0.8040 (mmm) cc_final: 0.7677 (mtp) REVERT: D 395 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (p) REVERT: D 410 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8761 (mmmt) REVERT: D 412 HIS cc_start: 0.6282 (t70) cc_final: 0.6074 (t70) REVERT: D 533 TYR cc_start: 0.8605 (t80) cc_final: 0.8297 (t80) REVERT: D 635 SER cc_start: 0.8951 (t) cc_final: 0.8734 (p) REVERT: D 650 LEU cc_start: 0.8388 (tp) cc_final: 0.8144 (tp) REVERT: D 702 TYR cc_start: 0.7747 (t80) cc_final: 0.7138 (t80) REVERT: D 714 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7441 (tp40) REVERT: D 760 ASP cc_start: 0.9467 (m-30) cc_final: 0.9041 (t70) REVERT: D 764 ASN cc_start: 0.9106 (m-40) cc_final: 0.8788 (m110) REVERT: D 783 LYS cc_start: 0.7335 (pmtt) cc_final: 0.6880 (ptpp) REVERT: E 27 HIS cc_start: 0.6832 (t-90) cc_final: 0.6595 (t-90) REVERT: E 59 ARG cc_start: 0.6999 (tmm-80) cc_final: 0.6663 (tmt-80) REVERT: E 75 HIS cc_start: 0.7453 (t70) cc_final: 0.6541 (t70) REVERT: E 94 ASN cc_start: 0.7672 (p0) cc_final: 0.7412 (p0) REVERT: E 95 ILE cc_start: 0.8136 (tp) cc_final: 0.7020 (tt) REVERT: E 99 PHE cc_start: 0.7789 (m-10) cc_final: 0.7534 (m-80) REVERT: E 101 HIS cc_start: 0.7278 (m170) cc_final: 0.6702 (m170) REVERT: F 33 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7047 (tm-30) REVERT: F 78 PHE cc_start: 0.7518 (m-80) cc_final: 0.7218 (m-80) REVERT: F 99 PHE cc_start: 0.7524 (m-10) cc_final: 0.7286 (m-80) REVERT: F 116 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6461 (pp-130) outliers start: 14 outliers final: 0 residues processed: 659 average time/residue: 0.3241 time to fit residues: 312.7072 Evaluate side-chains 387 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 384 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain F residue 116 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.1980 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 920 ASN B 411 ASN B 412 HIS B 435 HIS B 461 ASN C 435 HIS C 587 GLN C 726 ASN C 747 ASN C 920 ASN C 950 HIS D 411 ASN D 435 HIS D 461 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19427 Z= 0.193 Angle : 0.786 11.736 26060 Z= 0.401 Chirality : 0.044 0.185 2836 Planarity : 0.006 0.079 3142 Dihedral : 18.277 161.589 3219 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.41 % Favored : 89.71 % Rotamer: Outliers : 3.93 % Allowed : 16.45 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.86 % 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: -3.93 (0.15), residues: 2264 helix: -1.83 (0.12), residues: 1314 sheet: -4.12 (0.34), residues: 140 loop : -3.46 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 671 HIS 0.012 0.002 HIS E 107 PHE 0.033 0.002 PHE A 901 TYR 0.040 0.002 TYR D 450 ARG 0.006 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 482 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.8905 (ttp) cc_final: 0.8625 (ttm) REVERT: A 581 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 668 ASP cc_start: 0.7839 (m-30) cc_final: 0.7618 (p0) REVERT: A 924 MET cc_start: 0.7147 (mmm) cc_final: 0.6858 (mmp) REVERT: A 938 PHE cc_start: 0.8767 (m-10) cc_final: 0.8536 (m-80) REVERT: A 1003 TYR cc_start: 0.7433 (m-80) cc_final: 0.7161 (m-80) REVERT: A 1005 TRP cc_start: 0.5717 (m100) cc_final: 0.5451 (m-90) REVERT: A 1007 PHE cc_start: 0.8467 (m-80) cc_final: 0.8061 (m-80) REVERT: A 1016 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 1019 SER cc_start: 0.8821 (t) cc_final: 0.8597 (p) REVERT: B 479 LEU cc_start: 0.8844 (tp) cc_final: 0.8615 (tp) REVERT: B 484 VAL cc_start: 0.8769 (m) cc_final: 0.8525 (p) REVERT: B 493 LYS cc_start: 0.8934 (mttp) cc_final: 0.8628 (tttm) REVERT: B 619 ASN cc_start: 0.8764 (t0) cc_final: 0.8069 (t0) REVERT: B 669 LYS cc_start: 0.9180 (pttt) cc_final: 0.8955 (pttt) REVERT: B 714 GLN cc_start: 0.7447 (tp-100) cc_final: 0.6686 (tp40) REVERT: B 760 ASP cc_start: 0.9332 (m-30) cc_final: 0.8988 (t0) REVERT: B 765 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8560 (tttm) REVERT: C 450 TYR cc_start: 0.7187 (m-80) cc_final: 0.6371 (m-80) REVERT: C 463 MET cc_start: 0.9022 (ttp) cc_final: 0.8805 (ttm) REVERT: C 518 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 714 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 880 MET cc_start: 0.7370 (tmm) cc_final: 0.7105 (tmm) REVERT: C 926 ARG cc_start: 0.6447 (ttm-80) cc_final: 0.5678 (tmt170) REVERT: C 991 ARG cc_start: 0.6715 (mmt-90) cc_final: 0.6250 (mmt90) REVERT: C 1000 ASN cc_start: 0.7455 (m-40) cc_final: 0.6842 (m-40) REVERT: C 1029 MET cc_start: 0.7983 (mmm) cc_final: 0.7754 (mtp) REVERT: D 402 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6869 (mm-30) REVERT: D 419 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7857 (tp30) REVERT: D 421 TYR cc_start: 0.8016 (m-10) cc_final: 0.7803 (m-10) REVERT: D 463 MET cc_start: 0.7293 (ptp) cc_final: 0.7053 (ptp) REVERT: D 479 LEU cc_start: 0.8803 (tp) cc_final: 0.8565 (tp) REVERT: D 493 LYS cc_start: 0.8612 (mttp) cc_final: 0.8094 (tttm) REVERT: D 573 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8259 (tp) REVERT: D 714 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7322 (tp40) REVERT: D 748 LEU cc_start: 0.9609 (tp) cc_final: 0.9276 (pp) REVERT: D 760 ASP cc_start: 0.9532 (m-30) cc_final: 0.9062 (t70) REVERT: D 762 LEU cc_start: 0.9412 (mm) cc_final: 0.9210 (mm) REVERT: D 764 ASN cc_start: 0.9091 (m-40) cc_final: 0.8736 (m-40) REVERT: D 789 LEU cc_start: 0.8750 (tp) cc_final: 0.8422 (tt) REVERT: E 75 HIS cc_start: 0.7306 (t70) cc_final: 0.6383 (t70) REVERT: E 78 PHE cc_start: 0.7360 (m-80) cc_final: 0.7107 (m-80) REVERT: E 87 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7111 (mm-30) REVERT: E 94 ASN cc_start: 0.7597 (p0) cc_final: 0.7395 (p0) REVERT: E 95 ILE cc_start: 0.8313 (tp) cc_final: 0.7482 (tt) REVERT: E 101 HIS cc_start: 0.7200 (m170) cc_final: 0.6323 (m170) REVERT: F 78 PHE cc_start: 0.7453 (m-80) cc_final: 0.7217 (m-80) REVERT: F 108 ARG cc_start: 0.5197 (tpm170) cc_final: 0.4909 (mmm160) REVERT: F 123 MET cc_start: 0.6348 (mmm) cc_final: 0.6108 (mmm) REVERT: A 1108 GLU cc_start: 0.4819 (tp30) cc_final: 0.4533 (mm-30) outliers start: 77 outliers final: 28 residues processed: 529 average time/residue: 0.3125 time to fit residues: 247.6713 Evaluate side-chains 421 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 389 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 166 optimal weight: 10.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 619 ASN A 714 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 950 HIS ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19427 Z= 0.361 Angle : 0.815 9.718 26060 Z= 0.415 Chirality : 0.047 0.215 2836 Planarity : 0.006 0.084 3142 Dihedral : 17.497 151.662 3213 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.40 % Favored : 87.99 % Rotamer: Outliers : 4.85 % Allowed : 18.13 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 9.38 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.17), residues: 2264 helix: -0.87 (0.13), residues: 1334 sheet: -3.76 (0.36), residues: 132 loop : -3.39 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 460 HIS 0.013 0.002 HIS F 101 PHE 0.027 0.002 PHE E 146 TYR 0.039 0.002 TYR D 450 ARG 0.006 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 403 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8010 (mmm) cc_final: 0.7745 (mmm) REVERT: A 450 TYR cc_start: 0.7459 (m-80) cc_final: 0.7197 (m-80) REVERT: A 463 MET cc_start: 0.8981 (ttp) cc_final: 0.8763 (ttm) REVERT: A 581 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.8882 (tp) REVERT: A 585 MET cc_start: 0.8471 (mpt) cc_final: 0.8066 (mpt) REVERT: A 714 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8914 (mm-40) REVERT: A 924 MET cc_start: 0.7026 (mmm) cc_final: 0.6603 (mmm) REVERT: A 926 ARG cc_start: 0.7172 (ptm160) cc_final: 0.6738 (ptm160) REVERT: A 998 TYR cc_start: 0.7728 (p90) cc_final: 0.7393 (p90) REVERT: A 1000 ASN cc_start: 0.7982 (m-40) cc_final: 0.7252 (m-40) REVERT: A 1003 TYR cc_start: 0.7669 (m-80) cc_final: 0.7111 (m-80) REVERT: A 1005 TRP cc_start: 0.6223 (m100) cc_final: 0.5903 (m-90) REVERT: A 1019 SER cc_start: 0.9053 (t) cc_final: 0.8736 (p) REVERT: B 483 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8651 (mm) REVERT: B 493 LYS cc_start: 0.8945 (mttp) cc_final: 0.8692 (tttm) REVERT: B 626 VAL cc_start: 0.9385 (t) cc_final: 0.9108 (m) REVERT: B 713 GLU cc_start: 0.9102 (tt0) cc_final: 0.8643 (tm-30) REVERT: B 714 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7357 (tp40) REVERT: B 748 LEU cc_start: 0.9564 (tp) cc_final: 0.9274 (pp) REVERT: B 760 ASP cc_start: 0.9243 (m-30) cc_final: 0.8851 (t0) REVERT: B 764 ASN cc_start: 0.8730 (m-40) cc_final: 0.8108 (m-40) REVERT: C 450 TYR cc_start: 0.7556 (m-80) cc_final: 0.6833 (m-80) REVERT: C 518 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9166 (pp) REVERT: C 581 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9101 (tp) REVERT: C 890 CYS cc_start: 0.1760 (t) cc_final: 0.1354 (t) REVERT: C 926 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.5881 (tmt170) REVERT: C 991 ARG cc_start: 0.6696 (mmt-90) cc_final: 0.6188 (mmt90) REVERT: C 999 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6600 (m-10) REVERT: C 1000 ASN cc_start: 0.8061 (m-40) cc_final: 0.7393 (m110) REVERT: C 1005 TRP cc_start: 0.6928 (OUTLIER) cc_final: 0.6298 (t-100) REVERT: C 1029 MET cc_start: 0.8070 (mmm) cc_final: 0.7828 (mtp) REVERT: D 421 TYR cc_start: 0.8219 (m-10) cc_final: 0.7971 (m-10) REVERT: D 431 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: D 460 TRP cc_start: 0.6776 (m-90) cc_final: 0.6303 (m-90) REVERT: D 493 LYS cc_start: 0.8669 (mttp) cc_final: 0.7948 (tttm) REVERT: D 642 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8706 (tm-30) REVERT: D 714 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7753 (tm-30) REVERT: D 760 ASP cc_start: 0.9465 (m-30) cc_final: 0.9114 (t70) REVERT: D 763 LYS cc_start: 0.9291 (tppt) cc_final: 0.9032 (tppt) REVERT: E 75 HIS cc_start: 0.7474 (t70) cc_final: 0.6831 (t70) REVERT: E 99 PHE cc_start: 0.8077 (m-80) cc_final: 0.7769 (t80) REVERT: E 101 HIS cc_start: 0.7696 (m170) cc_final: 0.7399 (m-70) REVERT: E 134 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7162 (tm-30) REVERT: F 99 PHE cc_start: 0.7926 (m-80) cc_final: 0.7401 (t80) outliers start: 95 outliers final: 43 residues processed: 466 average time/residue: 0.3027 time to fit residues: 214.4567 Evaluate side-chains 405 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 354 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN F 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19427 Z= 0.233 Angle : 0.739 12.302 26060 Z= 0.371 Chirality : 0.044 0.208 2836 Planarity : 0.005 0.074 3142 Dihedral : 16.625 145.040 3213 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.69 % Favored : 88.83 % Rotamer: Outliers : 4.29 % Allowed : 20.84 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2264 helix: -0.21 (0.14), residues: 1312 sheet: -3.53 (0.35), residues: 154 loop : -3.35 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 460 HIS 0.016 0.002 HIS F 101 PHE 0.033 0.002 PHE A 943 TYR 0.038 0.002 TYR B 673 ARG 0.005 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 409 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7987 (mmm) cc_final: 0.7756 (mmm) REVERT: A 581 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8765 (tp) REVERT: A 585 MET cc_start: 0.8222 (mpt) cc_final: 0.7876 (mpt) REVERT: A 663 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7226 (tppt) REVERT: A 668 ASP cc_start: 0.8049 (p0) cc_final: 0.7518 (p0) REVERT: A 926 ARG cc_start: 0.7107 (ptm160) cc_final: 0.6719 (ptm160) REVERT: A 998 TYR cc_start: 0.7694 (p90) cc_final: 0.7344 (p90) REVERT: A 1000 ASN cc_start: 0.7959 (m-40) cc_final: 0.7093 (m-40) REVERT: A 1001 TYR cc_start: 0.8254 (p90) cc_final: 0.7897 (p90) REVERT: A 1003 TYR cc_start: 0.7615 (m-80) cc_final: 0.7009 (m-80) REVERT: A 1005 TRP cc_start: 0.6261 (m100) cc_final: 0.5931 (m-90) REVERT: A 1019 SER cc_start: 0.9049 (t) cc_final: 0.8753 (p) REVERT: B 401 LEU cc_start: 0.8911 (pp) cc_final: 0.8547 (tp) REVERT: B 541 PHE cc_start: 0.8682 (t80) cc_final: 0.8466 (t80) REVERT: B 577 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8555 (mp) REVERT: B 642 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 713 GLU cc_start: 0.9074 (tt0) cc_final: 0.8654 (tm-30) REVERT: B 721 MET cc_start: 0.8334 (ppp) cc_final: 0.8120 (ppp) REVERT: B 748 LEU cc_start: 0.9558 (tp) cc_final: 0.9267 (pp) REVERT: B 760 ASP cc_start: 0.9186 (m-30) cc_final: 0.8830 (t70) REVERT: B 764 ASN cc_start: 0.8721 (m-40) cc_final: 0.8200 (m-40) REVERT: C 450 TYR cc_start: 0.7545 (m-80) cc_final: 0.6704 (m-80) REVERT: C 458 LYS cc_start: 0.7545 (mmtm) cc_final: 0.7231 (mmtm) REVERT: C 518 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9082 (pp) REVERT: C 581 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8800 (tp) REVERT: C 585 MET cc_start: 0.8334 (mpt) cc_final: 0.7772 (mpt) REVERT: C 619 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.6958 (t0) REVERT: C 713 GLU cc_start: 0.8581 (pp20) cc_final: 0.8223 (pp20) REVERT: C 926 ARG cc_start: 0.6883 (ttm-80) cc_final: 0.5861 (tmt170) REVERT: C 991 ARG cc_start: 0.6629 (mmt-90) cc_final: 0.6205 (mmt90) REVERT: C 1000 ASN cc_start: 0.7892 (m-40) cc_final: 0.7141 (m-40) REVERT: C 1007 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: C 1029 MET cc_start: 0.8042 (mmm) cc_final: 0.7783 (mtp) REVERT: D 421 TYR cc_start: 0.8270 (m-10) cc_final: 0.8011 (m-10) REVERT: D 431 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: D 493 LYS cc_start: 0.8596 (mttp) cc_final: 0.7932 (mtpp) REVERT: D 642 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8589 (tm-30) REVERT: D 714 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7732 (tm-30) REVERT: D 748 LEU cc_start: 0.9651 (tp) cc_final: 0.9307 (pp) REVERT: D 760 ASP cc_start: 0.9450 (m-30) cc_final: 0.8987 (t0) REVERT: D 764 ASN cc_start: 0.9060 (m-40) cc_final: 0.8603 (m110) REVERT: D 781 LYS cc_start: 0.5505 (tptt) cc_final: 0.4291 (mtpp) REVERT: E 75 HIS cc_start: 0.7370 (t70) cc_final: 0.6795 (t70) REVERT: E 99 PHE cc_start: 0.8187 (m-80) cc_final: 0.7832 (t80) REVERT: E 101 HIS cc_start: 0.7624 (m170) cc_final: 0.7118 (m-70) REVERT: E 134 GLU cc_start: 0.7244 (tm-30) cc_final: 0.7028 (tm-30) REVERT: F 99 PHE cc_start: 0.7768 (m-80) cc_final: 0.7336 (t80) REVERT: F 108 ARG cc_start: 0.5624 (mmm160) cc_final: 0.5418 (mmm160) REVERT: A 1108 GLU cc_start: 0.5982 (tp30) cc_final: 0.5617 (mm-30) outliers start: 84 outliers final: 38 residues processed: 465 average time/residue: 0.2960 time to fit residues: 211.9122 Evaluate side-chains 409 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 364 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 GLN ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19427 Z= 0.243 Angle : 0.741 12.720 26060 Z= 0.372 Chirality : 0.044 0.231 2836 Planarity : 0.005 0.073 3142 Dihedral : 16.034 140.399 3213 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.00 % Favored : 88.56 % Rotamer: Outliers : 3.98 % Allowed : 22.83 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.77 % 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: -1.92 (0.18), residues: 2264 helix: 0.05 (0.14), residues: 1326 sheet: -3.15 (0.40), residues: 128 loop : -3.24 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 460 HIS 0.017 0.002 HIS F 101 PHE 0.030 0.002 PHE A 943 TYR 0.033 0.002 TYR D 450 ARG 0.005 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 380 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8053 (mmm) cc_final: 0.7846 (mmm) REVERT: A 581 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8801 (tp) REVERT: A 585 MET cc_start: 0.8196 (mpt) cc_final: 0.7856 (mpt) REVERT: A 755 GLU cc_start: 0.9194 (mp0) cc_final: 0.8698 (mp0) REVERT: A 1000 ASN cc_start: 0.7888 (m-40) cc_final: 0.6993 (m-40) REVERT: A 1003 TYR cc_start: 0.7576 (m-80) cc_final: 0.7298 (m-80) REVERT: A 1005 TRP cc_start: 0.6485 (m100) cc_final: 0.6066 (m-90) REVERT: A 1019 SER cc_start: 0.9138 (t) cc_final: 0.8806 (p) REVERT: B 401 LEU cc_start: 0.9029 (pp) cc_final: 0.8630 (tt) REVERT: B 431 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: B 713 GLU cc_start: 0.9086 (tt0) cc_final: 0.8641 (tm-30) REVERT: B 721 MET cc_start: 0.8489 (ppp) cc_final: 0.8151 (ppp) REVERT: B 760 ASP cc_start: 0.9209 (m-30) cc_final: 0.8737 (t70) REVERT: B 764 ASN cc_start: 0.8635 (m-40) cc_final: 0.7950 (m110) REVERT: C 450 TYR cc_start: 0.7615 (m-80) cc_final: 0.6693 (m-80) REVERT: C 518 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9110 (pp) REVERT: C 581 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8793 (tp) REVERT: C 585 MET cc_start: 0.8304 (mpt) cc_final: 0.7773 (mpt) REVERT: C 619 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.7047 (t0) REVERT: C 713 GLU cc_start: 0.8600 (pp20) cc_final: 0.8245 (pp20) REVERT: C 926 ARG cc_start: 0.6803 (ttm-80) cc_final: 0.5658 (tmt170) REVERT: C 1000 ASN cc_start: 0.7966 (m-40) cc_final: 0.7209 (m-40) REVERT: C 1005 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.6345 (t-100) REVERT: C 1007 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8533 (m-10) REVERT: C 1029 MET cc_start: 0.8041 (mmm) cc_final: 0.7795 (mtp) REVERT: D 401 LEU cc_start: 0.8874 (pp) cc_final: 0.8445 (tp) REVERT: D 421 TYR cc_start: 0.8244 (m-10) cc_final: 0.8022 (m-10) REVERT: D 431 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: D 460 TRP cc_start: 0.6681 (m-90) cc_final: 0.6270 (m-90) REVERT: D 493 LYS cc_start: 0.8526 (mttp) cc_final: 0.8021 (mtmt) REVERT: D 642 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8566 (tm-30) REVERT: D 714 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7709 (tm-30) REVERT: D 748 LEU cc_start: 0.9656 (tp) cc_final: 0.9335 (pp) REVERT: D 760 ASP cc_start: 0.9418 (m-30) cc_final: 0.9024 (t0) REVERT: E 101 HIS cc_start: 0.7636 (m170) cc_final: 0.7315 (m-70) outliers start: 78 outliers final: 50 residues processed: 431 average time/residue: 0.2927 time to fit residues: 194.0281 Evaluate side-chains 401 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 220 optimal weight: 0.0270 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19427 Z= 0.184 Angle : 0.708 12.838 26060 Z= 0.353 Chirality : 0.043 0.209 2836 Planarity : 0.005 0.070 3142 Dihedral : 15.268 133.846 3213 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.38 % Favored : 89.31 % Rotamer: Outliers : 4.14 % Allowed : 23.60 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 2264 helix: 0.42 (0.15), residues: 1318 sheet: -2.91 (0.36), residues: 158 loop : -3.22 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 460 HIS 0.019 0.002 HIS F 101 PHE 0.032 0.002 PHE A 943 TYR 0.029 0.002 TYR D 450 ARG 0.004 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 387 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7355 (pt0) REVERT: A 581 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8696 (tp) REVERT: A 585 MET cc_start: 0.8011 (mpt) cc_final: 0.7554 (mpt) REVERT: A 755 GLU cc_start: 0.9147 (mp0) cc_final: 0.8710 (mp0) REVERT: A 887 TRP cc_start: 0.8213 (m100) cc_final: 0.8010 (m100) REVERT: A 907 MET cc_start: 0.6023 (mmt) cc_final: 0.5815 (mmm) REVERT: A 938 PHE cc_start: 0.8808 (m-10) cc_final: 0.8592 (m-80) REVERT: A 988 MET cc_start: 0.8650 (mmp) cc_final: 0.8247 (mmm) REVERT: A 1000 ASN cc_start: 0.7808 (m-40) cc_final: 0.6982 (m-40) REVERT: A 1003 TYR cc_start: 0.7524 (m-80) cc_final: 0.7116 (m-80) REVERT: A 1005 TRP cc_start: 0.6489 (m100) cc_final: 0.6040 (m-90) REVERT: A 1019 SER cc_start: 0.9098 (t) cc_final: 0.8778 (p) REVERT: B 401 LEU cc_start: 0.9001 (pp) cc_final: 0.8597 (tt) REVERT: B 431 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: B 491 PHE cc_start: 0.6044 (OUTLIER) cc_final: 0.5798 (t80) REVERT: B 713 GLU cc_start: 0.9097 (tt0) cc_final: 0.8601 (tm-30) REVERT: B 721 MET cc_start: 0.8489 (ppp) cc_final: 0.8082 (ppp) REVERT: B 748 LEU cc_start: 0.9454 (tp) cc_final: 0.9190 (pp) REVERT: B 760 ASP cc_start: 0.9172 (m-30) cc_final: 0.8694 (t70) REVERT: B 764 ASN cc_start: 0.8586 (m-40) cc_final: 0.7976 (m110) REVERT: C 450 TYR cc_start: 0.7569 (m-80) cc_final: 0.6613 (m-80) REVERT: C 518 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9046 (pp) REVERT: C 581 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8702 (tp) REVERT: C 585 MET cc_start: 0.8230 (mpt) cc_final: 0.7632 (mpt) REVERT: C 619 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.7040 (t0) REVERT: C 688 GLU cc_start: 0.8153 (pt0) cc_final: 0.7345 (tp30) REVERT: C 713 GLU cc_start: 0.8644 (pp20) cc_final: 0.8294 (pp20) REVERT: C 865 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6559 (mm-30) REVERT: C 926 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.5668 (tmt170) REVERT: C 998 TYR cc_start: 0.8275 (p90) cc_final: 0.7853 (p90) REVERT: C 1000 ASN cc_start: 0.7850 (m-40) cc_final: 0.7194 (m-40) REVERT: C 1007 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8624 (m-10) REVERT: C 1029 MET cc_start: 0.8034 (mmm) cc_final: 0.7748 (mtp) REVERT: D 401 LEU cc_start: 0.8993 (pp) cc_final: 0.8718 (tt) REVERT: D 421 TYR cc_start: 0.8192 (m-10) cc_final: 0.7970 (m-10) REVERT: D 431 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: D 434 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9001 (ptpp) REVERT: D 450 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.3869 (m-80) REVERT: D 493 LYS cc_start: 0.8538 (mttp) cc_final: 0.8001 (mtmt) REVERT: D 642 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8504 (tm-30) REVERT: D 714 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7655 (tm-30) REVERT: D 760 ASP cc_start: 0.9365 (m-30) cc_final: 0.8943 (t0) REVERT: E 75 HIS cc_start: 0.7126 (t70) cc_final: 0.6585 (t70) REVERT: E 101 HIS cc_start: 0.7717 (m170) cc_final: 0.7330 (m-70) REVERT: F 123 MET cc_start: 0.6169 (mmm) cc_final: 0.5956 (mmm) REVERT: F 147 PHE cc_start: 0.8651 (m-80) cc_final: 0.8342 (m-80) outliers start: 81 outliers final: 49 residues processed: 439 average time/residue: 0.2892 time to fit residues: 197.8191 Evaluate side-chains 417 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 359 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 123 optimal weight: 0.0670 chunk 219 optimal weight: 0.6980 chunk 137 optimal weight: 0.0070 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19427 Z= 0.179 Angle : 0.719 13.905 26060 Z= 0.355 Chirality : 0.043 0.207 2836 Planarity : 0.005 0.066 3142 Dihedral : 14.671 126.204 3213 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.47 % Favored : 89.36 % Rotamer: Outliers : 3.68 % Allowed : 24.46 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.45 % 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: -1.23 (0.19), residues: 2264 helix: 0.73 (0.15), residues: 1288 sheet: -2.44 (0.36), residues: 172 loop : -3.09 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 887 HIS 0.016 0.002 HIS F 101 PHE 0.033 0.002 PHE A 943 TYR 0.029 0.002 TYR D 450 ARG 0.011 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 385 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7411 (pt0) REVERT: A 581 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8705 (tp) REVERT: A 585 MET cc_start: 0.7995 (mpt) cc_final: 0.7573 (mpt) REVERT: A 755 GLU cc_start: 0.9163 (mp0) cc_final: 0.8751 (mp0) REVERT: A 926 ARG cc_start: 0.6509 (ptm160) cc_final: 0.6142 (ptm160) REVERT: A 988 MET cc_start: 0.8665 (mmp) cc_final: 0.8350 (mmm) REVERT: A 1000 ASN cc_start: 0.7808 (m-40) cc_final: 0.7110 (m110) REVERT: A 1003 TYR cc_start: 0.7480 (m-80) cc_final: 0.7199 (m-80) REVERT: A 1005 TRP cc_start: 0.6507 (m100) cc_final: 0.6084 (m-90) REVERT: A 1019 SER cc_start: 0.9095 (t) cc_final: 0.8772 (p) REVERT: B 401 LEU cc_start: 0.9075 (pp) cc_final: 0.8731 (tt) REVERT: B 431 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: B 491 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5938 (t80) REVERT: B 713 GLU cc_start: 0.9121 (tt0) cc_final: 0.8559 (tm-30) REVERT: B 721 MET cc_start: 0.8567 (ppp) cc_final: 0.8099 (ppp) REVERT: B 748 LEU cc_start: 0.9486 (tp) cc_final: 0.9185 (pp) REVERT: B 760 ASP cc_start: 0.9145 (m-30) cc_final: 0.8626 (t70) REVERT: B 764 ASN cc_start: 0.8621 (m-40) cc_final: 0.7922 (m110) REVERT: C 450 TYR cc_start: 0.7466 (m-80) cc_final: 0.7117 (m-80) REVERT: C 518 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9087 (pp) REVERT: C 581 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8650 (tp) REVERT: C 585 MET cc_start: 0.8216 (mpt) cc_final: 0.7718 (mpt) REVERT: C 688 GLU cc_start: 0.8090 (pt0) cc_final: 0.7301 (tp30) REVERT: C 713 GLU cc_start: 0.8668 (pp20) cc_final: 0.8272 (pp20) REVERT: C 714 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8519 (mm110) REVERT: C 926 ARG cc_start: 0.6757 (ttm-80) cc_final: 0.5850 (tmt170) REVERT: C 968 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (mp) REVERT: C 998 TYR cc_start: 0.8275 (p90) cc_final: 0.7791 (p90) REVERT: C 1000 ASN cc_start: 0.7741 (m-40) cc_final: 0.7121 (m-40) REVERT: C 1007 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: C 1029 MET cc_start: 0.8025 (mmm) cc_final: 0.7770 (mtp) REVERT: D 431 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: D 434 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9026 (ptpp) REVERT: D 450 TYR cc_start: 0.5278 (OUTLIER) cc_final: 0.4326 (m-80) REVERT: D 493 LYS cc_start: 0.8604 (mttp) cc_final: 0.8033 (mtmt) REVERT: D 714 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7453 (tp40) REVERT: D 760 ASP cc_start: 0.9331 (m-30) cc_final: 0.8783 (t0) REVERT: D 764 ASN cc_start: 0.8976 (m-40) cc_final: 0.8423 (m-40) REVERT: E 75 HIS cc_start: 0.7096 (t70) cc_final: 0.6588 (t70) REVERT: E 101 HIS cc_start: 0.7736 (m170) cc_final: 0.7265 (m-70) REVERT: E 123 MET cc_start: 0.5961 (mmm) cc_final: 0.5677 (mmm) REVERT: F 147 PHE cc_start: 0.8506 (m-80) cc_final: 0.8222 (m-80) outliers start: 72 outliers final: 49 residues processed: 427 average time/residue: 0.2890 time to fit residues: 191.7125 Evaluate side-chains 407 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1025 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 450 TYR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 587 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19427 Z= 0.374 Angle : 0.806 16.807 26060 Z= 0.405 Chirality : 0.047 0.198 2836 Planarity : 0.005 0.070 3142 Dihedral : 15.382 131.136 3213 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.53 % Favored : 88.25 % Rotamer: Outliers : 4.34 % Allowed : 24.82 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 7.81 % Twisted General : 0.41 % 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: -1.45 (0.18), residues: 2264 helix: 0.46 (0.15), residues: 1336 sheet: -2.76 (0.37), residues: 172 loop : -3.15 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 887 HIS 0.012 0.002 HIS F 101 PHE 0.035 0.002 PHE A 943 TYR 0.029 0.002 TYR B 450 ARG 0.006 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 351 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8929 (tp) REVERT: A 755 GLU cc_start: 0.9175 (mp0) cc_final: 0.8733 (mp0) REVERT: A 891 PHE cc_start: 0.6397 (m-80) cc_final: 0.5900 (m-80) REVERT: A 899 ARG cc_start: 0.8114 (mpp80) cc_final: 0.7375 (mpp80) REVERT: A 926 ARG cc_start: 0.6752 (ptm160) cc_final: 0.6392 (ptm160) REVERT: A 988 MET cc_start: 0.8689 (mmp) cc_final: 0.8378 (mmm) REVERT: A 1000 ASN cc_start: 0.7931 (m-40) cc_final: 0.7120 (m110) REVERT: A 1003 TYR cc_start: 0.7784 (m-80) cc_final: 0.7472 (m-80) REVERT: A 1019 SER cc_start: 0.9247 (t) cc_final: 0.8902 (p) REVERT: B 401 LEU cc_start: 0.9123 (pp) cc_final: 0.8739 (tt) REVERT: B 431 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: B 491 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.6154 (t80) REVERT: B 713 GLU cc_start: 0.9119 (tt0) cc_final: 0.8699 (tm-30) REVERT: B 721 MET cc_start: 0.8635 (ppp) cc_final: 0.8115 (ppp) REVERT: B 748 LEU cc_start: 0.9510 (tp) cc_final: 0.9216 (pp) REVERT: B 760 ASP cc_start: 0.9148 (m-30) cc_final: 0.8666 (t70) REVERT: B 764 ASN cc_start: 0.8740 (m-40) cc_final: 0.8062 (m110) REVERT: C 450 TYR cc_start: 0.7715 (m-80) cc_final: 0.7065 (m-80) REVERT: C 518 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9176 (pp) REVERT: C 581 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.8852 (tp) REVERT: C 585 MET cc_start: 0.8348 (mpt) cc_final: 0.7736 (mpt) REVERT: C 619 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.6611 (t0) REVERT: C 688 GLU cc_start: 0.8249 (pt0) cc_final: 0.7516 (tp30) REVERT: C 781 LYS cc_start: 0.7737 (mppt) cc_final: 0.7163 (pttp) REVERT: C 926 ARG cc_start: 0.6764 (ttm-80) cc_final: 0.5912 (tmt170) REVERT: C 968 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8593 (mp) REVERT: C 998 TYR cc_start: 0.8263 (p90) cc_final: 0.7960 (p90) REVERT: C 999 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: C 1000 ASN cc_start: 0.7937 (m-40) cc_final: 0.7392 (m-40) REVERT: C 1005 TRP cc_start: 0.6893 (OUTLIER) cc_final: 0.6393 (t-100) REVERT: C 1029 MET cc_start: 0.8119 (mmm) cc_final: 0.7819 (mtp) REVERT: D 401 LEU cc_start: 0.9107 (pp) cc_final: 0.8725 (tt) REVERT: D 431 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: D 434 LYS cc_start: 0.9288 (mmmt) cc_final: 0.9062 (ptpp) REVERT: D 491 PHE cc_start: 0.6601 (OUTLIER) cc_final: 0.6378 (t80) REVERT: D 642 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 714 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7760 (tm-30) REVERT: D 760 ASP cc_start: 0.9337 (m-30) cc_final: 0.8906 (t0) REVERT: E 75 HIS cc_start: 0.7162 (t70) cc_final: 0.6865 (t70) REVERT: E 101 HIS cc_start: 0.7927 (m170) cc_final: 0.7539 (m-70) REVERT: F 99 PHE cc_start: 0.7431 (m-80) cc_final: 0.7138 (t80) REVERT: F 151 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6584 (t80) outliers start: 85 outliers final: 54 residues processed: 406 average time/residue: 0.3043 time to fit residues: 193.0406 Evaluate side-chains 394 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 328 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 878 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 999 PHE Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 491 PHE Chi-restraints excluded: chain D residue 495 PHE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.8980 chunk 210 optimal weight: 0.0970 chunk 192 optimal weight: 0.0670 chunk 204 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19427 Z= 0.200 Angle : 0.756 15.884 26060 Z= 0.376 Chirality : 0.044 0.191 2836 Planarity : 0.005 0.096 3142 Dihedral : 14.609 126.019 3213 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.98 % Favored : 89.80 % Rotamer: Outliers : 3.88 % Allowed : 25.64 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 4.69 % Twisted General : 0.41 % 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: -1.25 (0.19), residues: 2264 helix: 0.74 (0.15), residues: 1316 sheet: -2.49 (0.38), residues: 164 loop : -3.28 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 887 HIS 0.014 0.001 HIS F 101 PHE 0.034 0.002 PHE A 943 TYR 0.036 0.001 TYR B 450 ARG 0.007 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 351 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8545 (tp) REVERT: A 585 MET cc_start: 0.7918 (mpt) cc_final: 0.7245 (mpt) REVERT: A 755 GLU cc_start: 0.9133 (mp0) cc_final: 0.8732 (mp0) REVERT: A 899 ARG cc_start: 0.8071 (mpp80) cc_final: 0.7815 (mpp80) REVERT: A 926 ARG cc_start: 0.6480 (ptm160) cc_final: 0.6134 (ptm160) REVERT: A 988 MET cc_start: 0.8699 (mmp) cc_final: 0.8411 (mmm) REVERT: A 1000 ASN cc_start: 0.7794 (m-40) cc_final: 0.6960 (m-40) REVERT: A 1019 SER cc_start: 0.9187 (t) cc_final: 0.8881 (p) REVERT: B 431 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: B 491 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5951 (t80) REVERT: B 713 GLU cc_start: 0.9115 (tt0) cc_final: 0.8666 (tm-30) REVERT: B 721 MET cc_start: 0.8589 (ppp) cc_final: 0.8162 (ppp) REVERT: B 748 LEU cc_start: 0.9494 (tp) cc_final: 0.9211 (pp) REVERT: B 760 ASP cc_start: 0.9111 (m-30) cc_final: 0.8590 (t70) REVERT: B 764 ASN cc_start: 0.8741 (m-40) cc_final: 0.8046 (m110) REVERT: C 518 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9029 (pp) REVERT: C 581 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8577 (tp) REVERT: C 585 MET cc_start: 0.8181 (mpt) cc_final: 0.7539 (mpt) REVERT: C 619 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.6681 (t0) REVERT: C 688 GLU cc_start: 0.8103 (pt0) cc_final: 0.7364 (tp30) REVERT: C 713 GLU cc_start: 0.8683 (pp20) cc_final: 0.8303 (pp20) REVERT: C 924 MET cc_start: 0.6912 (mmm) cc_final: 0.6618 (mmp) REVERT: C 926 ARG cc_start: 0.6627 (ttm-80) cc_final: 0.5849 (tmt170) REVERT: C 998 TYR cc_start: 0.8253 (p90) cc_final: 0.7724 (p90) REVERT: C 1000 ASN cc_start: 0.7725 (m-40) cc_final: 0.7128 (m-40) REVERT: C 1029 MET cc_start: 0.7964 (mmm) cc_final: 0.7737 (mtp) REVERT: D 401 LEU cc_start: 0.9112 (pp) cc_final: 0.8658 (tt) REVERT: D 431 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: D 434 LYS cc_start: 0.9299 (mmmt) cc_final: 0.8977 (ptpp) REVERT: D 637 GLU cc_start: 0.8693 (pt0) cc_final: 0.8288 (pm20) REVERT: D 642 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 714 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7563 (tm-30) REVERT: D 744 THR cc_start: 0.9014 (m) cc_final: 0.8798 (p) REVERT: D 760 ASP cc_start: 0.9304 (m-30) cc_final: 0.8816 (t0) REVERT: E 75 HIS cc_start: 0.7099 (t70) cc_final: 0.6734 (t70) REVERT: E 101 HIS cc_start: 0.7733 (m170) cc_final: 0.7290 (m-70) REVERT: E 123 MET cc_start: 0.5840 (mmm) cc_final: 0.5180 (mmm) REVERT: F 114 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6731 (tm-30) REVERT: F 151 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6358 (t80) outliers start: 76 outliers final: 51 residues processed: 401 average time/residue: 0.2882 time to fit residues: 180.7936 Evaluate side-chains 393 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 334 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 491 PHE Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 0.3980 chunk 227 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19427 Z= 0.248 Angle : 0.765 14.227 26060 Z= 0.379 Chirality : 0.045 0.208 2836 Planarity : 0.005 0.089 3142 Dihedral : 14.446 125.526 3213 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.13 % Favored : 88.74 % Rotamer: Outliers : 3.68 % Allowed : 26.20 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.41 % 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: -1.19 (0.19), residues: 2264 helix: 0.69 (0.15), residues: 1334 sheet: -2.03 (0.42), residues: 152 loop : -3.24 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 887 HIS 0.012 0.002 HIS F 101 PHE 0.034 0.002 PHE A 943 TYR 0.039 0.002 TYR B 450 ARG 0.007 0.000 ARG B 715 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 344 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 585 MET cc_start: 0.8010 (mpt) cc_final: 0.7250 (mpt) REVERT: A 755 GLU cc_start: 0.9126 (mp0) cc_final: 0.8894 (mp0) REVERT: A 899 ARG cc_start: 0.8105 (mpp80) cc_final: 0.7642 (mpp80) REVERT: A 988 MET cc_start: 0.8722 (mmp) cc_final: 0.8410 (mmm) REVERT: A 1000 ASN cc_start: 0.7856 (m-40) cc_final: 0.7034 (m110) REVERT: A 1019 SER cc_start: 0.9194 (t) cc_final: 0.8886 (p) REVERT: B 431 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: B 713 GLU cc_start: 0.9144 (tt0) cc_final: 0.8647 (tm-30) REVERT: B 721 MET cc_start: 0.8616 (ppp) cc_final: 0.8124 (ppp) REVERT: B 748 LEU cc_start: 0.9499 (tp) cc_final: 0.9214 (pp) REVERT: B 760 ASP cc_start: 0.9120 (m-30) cc_final: 0.8591 (t70) REVERT: B 764 ASN cc_start: 0.8741 (m-40) cc_final: 0.8067 (m110) REVERT: C 450 TYR cc_start: 0.7066 (m-80) cc_final: 0.6788 (m-10) REVERT: C 518 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9117 (pp) REVERT: C 581 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8716 (tp) REVERT: C 585 MET cc_start: 0.8285 (mpt) cc_final: 0.7749 (mpt) REVERT: C 619 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.6745 (t0) REVERT: C 688 GLU cc_start: 0.8121 (pt0) cc_final: 0.7382 (tp30) REVERT: C 781 LYS cc_start: 0.7737 (mppt) cc_final: 0.7188 (pttp) REVERT: C 924 MET cc_start: 0.6880 (mmm) cc_final: 0.6581 (mmp) REVERT: C 926 ARG cc_start: 0.6662 (ttm-80) cc_final: 0.5909 (tmt170) REVERT: C 998 TYR cc_start: 0.8233 (p90) cc_final: 0.7739 (p90) REVERT: C 1000 ASN cc_start: 0.7715 (m-40) cc_final: 0.7125 (m-40) REVERT: C 1005 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.6441 (t-100) REVERT: D 431 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: D 434 LYS cc_start: 0.9320 (mmmt) cc_final: 0.9036 (ptpp) REVERT: D 637 GLU cc_start: 0.8675 (pt0) cc_final: 0.8189 (pm20) REVERT: D 642 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8248 (tm-30) REVERT: D 714 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7583 (tm-30) REVERT: D 760 ASP cc_start: 0.9301 (m-30) cc_final: 0.8814 (t0) REVERT: E 75 HIS cc_start: 0.7139 (t70) cc_final: 0.6877 (t70) REVERT: E 99 PHE cc_start: 0.8197 (m-10) cc_final: 0.7883 (t80) REVERT: E 101 HIS cc_start: 0.7964 (m170) cc_final: 0.7446 (m-70) REVERT: E 123 MET cc_start: 0.5789 (mmm) cc_final: 0.5134 (mmm) REVERT: F 99 PHE cc_start: 0.7351 (m-80) cc_final: 0.6982 (t80) REVERT: F 151 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.6407 (t80) outliers start: 72 outliers final: 56 residues processed: 388 average time/residue: 0.2869 time to fit residues: 172.6623 Evaluate side-chains 402 residues out of total 1958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 338 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 469 TYR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 GLU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 495 PHE Chi-restraints excluded: chain B residue 682 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 469 TYR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 619 ASN Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 900 CYS Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 1005 TRP Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 TYR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 151 TYR Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 151 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 chunk 26 optimal weight: 0.0040 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.165853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111557 restraints weight = 33594.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114419 restraints weight = 19639.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.114080 restraints weight = 14168.686| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19427 Z= 0.230 Angle : 0.761 14.629 26060 Z= 0.377 Chirality : 0.045 0.211 2836 Planarity : 0.005 0.088 3142 Dihedral : 14.112 124.541 3213 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.47 % Favored : 89.31 % Rotamer: Outliers : 3.52 % Allowed : 26.51 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.41 % 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: -1.24 (0.19), residues: 2264 helix: 0.70 (0.15), residues: 1324 sheet: -2.23 (0.40), residues: 162 loop : -3.27 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 887 HIS 0.012 0.001 HIS F 101 PHE 0.032 0.002 PHE A1028 TYR 0.040 0.002 TYR B 450 ARG 0.006 0.000 ARG B 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4478.35 seconds wall clock time: 82 minutes 37.94 seconds (4957.94 seconds total)