Starting phenix.real_space_refine on Sat Feb 17 21:48:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss3_40742/02_2024/8ss3_40742_updated.pdb" } resolution = 3.21 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= 0.049 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 S 130 5.16 5 C 13297 2.51 5 N 2919 2.21 5 O 3499 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 660": "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" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19887 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4671 Classifications: {'peptide': 596} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 578} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 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: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 613 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 12, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 358 Unusual residues: {'PCW': 10, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 449 Unusual residues: {'AJP': 3, 'CLR': 2, 'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-2': 2, 'PCW:plan-3': 5, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 307 Unusual residues: {'PCW': 9, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 47 Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 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: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'PCW': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 167 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 Time building chain proxies: 11.40, per 1000 atoms: 0.57 Number of scatterers: 19887 At special positions: 0 Unit cell: (118.69, 130.31, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 30 15.00 F 12 9.00 O 3499 8.00 N 2919 7.00 C 13297 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 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: 7.84 Conformation dependent library (CDL) restraints added in 3.0 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 16 sheets defined 52.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 517 through 520 Proline residue: A 520 - end of helix No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 523 through 542 removed outlier: 3.831A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.631A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 629 removed outlier: 3.575A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.588A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 741 through 756 removed outlier: 4.338A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.625A pdb=" N LEU A 748 " --> pdb=" O PRO A 745 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 751 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 755 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 756 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.763A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 821 removed outlier: 3.544A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 857 removed outlier: 3.526A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.995A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 988 removed outlier: 3.508A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1034 removed outlier: 3.763A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 436 removed outlier: 3.594A pdb=" N ALA B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 520 Proline residue: B 520 - end of helix Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.525A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.643A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 625 removed outlier: 3.661A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 666 through 676 removed outlier: 3.854A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 694 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.644A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 766 removed outlier: 3.511A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 517 through 520 Proline residue: C 520 - end of helix No H-bonds generated for 'chain 'C' and resid 517 through 520' Processing helix chain 'C' and resid 523 through 542 removed outlier: 3.831A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 584 removed outlier: 3.631A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 629 removed outlier: 3.575A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.588A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 741 through 756 removed outlier: 4.338A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.625A pdb=" N LEU C 748 " --> pdb=" O PRO C 745 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 750 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 751 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 755 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 removed outlier: 3.763A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 821 removed outlier: 3.545A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 819 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 857 removed outlier: 3.526A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 951 removed outlier: 3.996A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 988 removed outlier: 3.507A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP C 986 " --> pdb=" O SER C 982 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1034 removed outlier: 3.763A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 436 removed outlier: 3.595A pdb=" N ALA D 429 " --> pdb=" O CYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 520 Proline residue: D 520 - end of helix Processing helix chain 'D' and resid 523 through 545 removed outlier: 3.525A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.643A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 removed outlier: 3.661A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 666 through 676 removed outlier: 3.853A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 694 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.643A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 766 removed outlier: 3.512A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 5 through 36 removed outlier: 3.892A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE E 31 " --> pdb=" O HIS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.675A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 65 " --> pdb=" O CYS E 61 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 84 removed outlier: 3.598A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 106 removed outlier: 3.614A pdb=" N ASN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 125 through 158 removed outlier: 3.626A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 36 removed outlier: 3.892A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE F 31 " --> pdb=" O HIS F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.675A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG F 65 " --> pdb=" O CYS F 61 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.598A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 removed outlier: 3.614A pdb=" N ASN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 125 through 158 removed outlier: 3.627A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS F 137 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 720 through 723 removed outlier: 4.239A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 997 through 1003 removed outlier: 3.726A pdb=" N TYR A 998 " --> pdb=" O GLY A 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 865 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 870 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 876 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 888 through 890 Processing sheet with id= F, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.373A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 397 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.383A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.073A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.240A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 997 through 1003 removed outlier: 3.726A pdb=" N TYR C 998 " --> pdb=" O GLY C 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 865 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 870 " --> pdb=" O THR C 876 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR C 876 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 888 through 890 Processing sheet with id= N, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.372A pdb=" N LYS D 439 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL D 397 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.864A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.384A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2430 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: 5.61 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.02 - 0.46: 5 0.46 - 0.90: 6 0.90 - 1.34: 5363 1.34 - 1.78: 14681 1.78 - 2.22: 253 Warning: very small bond lengths. Bond restraints: 20308 Sorted by residual: bond pdb=" C27 AJP C1110 " pdb=" O78 AJP C1110 " ideal model delta sigma weight residual 1.406 0.016 1.390 2.00e-02 2.50e+03 4.83e+03 bond pdb=" C27 AJP A1111 " pdb=" O78 AJP A1111 " ideal model delta sigma weight residual 1.406 0.048 1.358 2.00e-02 2.50e+03 4.61e+03 bond pdb=" C27 AJP C1114 " pdb=" O78 AJP C1114 " ideal model delta sigma weight residual 1.406 0.058 1.348 2.00e-02 2.50e+03 4.54e+03 bond pdb=" C27 AJP A1110 " pdb=" O78 AJP A1110 " ideal model delta sigma weight residual 1.406 0.070 1.336 2.00e-02 2.50e+03 4.46e+03 bond pdb=" C27 AJP A1116 " pdb=" O78 AJP A1116 " ideal model delta sigma weight residual 1.406 0.088 1.318 2.00e-02 2.50e+03 4.34e+03 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 86.65 - 96.75: 17 96.75 - 106.85: 719 106.85 - 116.95: 13522 116.95 - 127.05: 12758 127.05 - 137.15: 248 Bond angle restraints: 27264 Sorted by residual: angle pdb=" C17 CLR A1107 " pdb=" C13 CLR A1107 " pdb=" C18 CLR A1107 " ideal model delta sigma weight residual 110.18 86.65 23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" C17 CLR C1106 " pdb=" C13 CLR C1106 " pdb=" C18 CLR C1106 " ideal model delta sigma weight residual 110.18 86.77 23.41 3.00e+00 1.11e-01 6.09e+01 angle pdb=" C17 CLR A1112 " pdb=" C13 CLR A1112 " pdb=" C18 CLR A1112 " ideal model delta sigma weight residual 110.18 88.52 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N VAL B 514 " pdb=" CA VAL B 514 " pdb=" C VAL B 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.14e+01 angle pdb=" N VAL D 514 " pdb=" CA VAL D 514 " pdb=" C VAL D 514 " ideal model delta sigma weight residual 112.83 105.74 7.09 9.90e-01 1.02e+00 5.13e+01 ... (remaining 27259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12006 35.97 - 71.94: 635 71.94 - 107.91: 187 107.91 - 143.88: 97 143.88 - 179.85: 48 Dihedral angle restraints: 12973 sinusoidal: 6391 harmonic: 6582 Sorted by residual: dihedral pdb=" CA PRO F 109 " pdb=" C PRO F 109 " pdb=" N ALA F 110 " pdb=" CA ALA F 110 " ideal model delta harmonic sigma weight residual -180.00 -118.55 -61.45 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PRO E 109 " pdb=" C PRO E 109 " pdb=" N ALA E 110 " pdb=" CA ALA E 110 " ideal model delta harmonic sigma weight residual -180.00 -118.58 -61.42 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.86 59.14 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 12970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 2878 1.098 - 2.196: 14 2.196 - 3.294: 11 3.294 - 4.392: 16 4.392 - 5.489: 42 Chirality restraints: 2961 Sorted by residual: chirality pdb=" C15 AJP A1110 " pdb=" C14 AJP A1110 " pdb=" C16 AJP A1110 " pdb=" C20 AJP A1110 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C15 AJP C1109 " pdb=" C14 AJP C1109 " pdb=" C16 AJP C1109 " pdb=" C20 AJP C1109 " both_signs ideal model delta sigma weight residual False -2.42 3.07 -5.49 2.00e-01 2.50e+01 7.53e+02 chirality pdb=" C02 AJP A1110 " pdb=" C01 AJP A1110 " pdb=" C03 AJP A1110 " pdb=" C85 AJP A1110 " both_signs ideal model delta sigma weight residual False 2.60 -2.84 5.44 2.00e-01 2.50e+01 7.40e+02 ... (remaining 2958 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C MET E 116 " -0.048 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C MET F 116 " 0.048 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 406 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C VAL D 406 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL D 406 " -0.017 2.00e-02 2.50e+03 pdb=" N MET D 407 " -0.015 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 540 2.68 - 3.23: 17787 3.23 - 3.79: 29818 3.79 - 4.34: 41568 4.34 - 4.90: 68211 Nonbonded interactions: 157924 Sorted by model distance: nonbonded pdb=" OE2 GLU C 705 " pdb=" OH TYR C 732 " model vdw 2.123 2.440 nonbonded pdb=" OE2 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.123 2.440 nonbonded pdb=" O25 AJP A1111 " pdb=" O79 AJP A1111 " model vdw 2.172 2.432 nonbonded pdb=" O25 AJP C1110 " pdb=" O79 AJP C1110 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP A1110 " pdb=" O78 AJP A1110 " model vdw 2.196 2.432 ... (remaining 157919 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 392 through 1035 or resid 1101 through 1104 or (resid 1105 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or na \ me C19 or name C20 or name C21 or name C22 or name C23)) or resid 1108 or resid \ 1110 or (resid 1113 and (name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23)) or r \ esid 1115)) selection = (chain 'C' and (resid 392 through 1035 or resid 1101 through 1105 or resid 1108 \ or resid 1110 or resid 1113 or resid 1115)) } ncs_group { reference = (chain 'B' and (resid 392 through 820 or resid 1101 through 1109 or (resid 1110 \ and (name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23)))) selection = (chain 'D' and (resid 392 through 820 or resid 1101 through 1108 or (resid 1109 \ through 1110 and (name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C18 or name C19 or name C20 or name C21 or name C22 or name C23)))) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or resid 201 or (resid 202 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ )) or resid 204 through 205)) selection = (chain 'F' and (resid 2 through 159 or resid 201 or (resid 202 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ )) or resid 204 through 205)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.010 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 52.230 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.047 1.390 20308 Z= 2.747 Angle : 1.899 23.526 27264 Z= 0.848 Chirality : 0.688 5.489 2961 Planarity : 0.007 0.062 3162 Dihedral : 28.238 179.849 8747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.59 % Favored : 91.70 % Rotamer: Outliers : 0.52 % Allowed : 3.92 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: -6.01 (0.11), residues: 2240 helix: -4.03 (0.07), residues: 1304 sheet: -3.28 (0.29), residues: 216 loop : -3.62 (0.17), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 861 HIS 0.007 0.002 HIS E 27 PHE 0.033 0.003 PHE A 574 TYR 0.033 0.003 TYR C 702 ARG 0.006 0.001 ARG C 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 511 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.8768 (mptp) cc_final: 0.8485 (mttt) REVERT: A 674 MET cc_start: 0.8782 (mtm) cc_final: 0.8517 (mtp) REVERT: A 1005 TRP cc_start: 0.8230 (p-90) cc_final: 0.7932 (p-90) REVERT: B 638 ASP cc_start: 0.8032 (m-30) cc_final: 0.7796 (m-30) REVERT: B 642 GLN cc_start: 0.8075 (pp30) cc_final: 0.7471 (pp30) REVERT: C 519 ASP cc_start: 0.8612 (m-30) cc_final: 0.8408 (m-30) REVERT: C 630 VAL cc_start: 0.8564 (t) cc_final: 0.8361 (m) REVERT: C 674 MET cc_start: 0.8866 (mtm) cc_final: 0.8641 (mtp) REVERT: C 1005 TRP cc_start: 0.8137 (p-90) cc_final: 0.7896 (p-90) REVERT: D 527 MET cc_start: 0.7638 (mmm) cc_final: 0.7387 (mmt) REVERT: D 657 GLU cc_start: 0.7760 (tp30) cc_final: 0.7496 (mm-30) REVERT: D 661 ARG cc_start: 0.7850 (ptt180) cc_final: 0.7637 (ttp-170) REVERT: D 770 LYS cc_start: 0.7660 (mmtp) cc_final: 0.7437 (tttp) REVERT: F 64 LEU cc_start: 0.8041 (mt) cc_final: 0.7837 (mt) outliers start: 10 outliers final: 0 residues processed: 519 average time/residue: 0.3456 time to fit residues: 265.3949 Evaluate side-chains 295 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 508 GLN A 575 ASN A 747 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN C 412 HIS C 575 ASN C 747 ASN C 947 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN E 75 HIS E 94 ASN E 124 ASN E 132 GLN F 94 ASN F 124 ASN F 132 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20308 Z= 0.237 Angle : 1.313 32.729 27264 Z= 0.512 Chirality : 0.151 2.450 2961 Planarity : 0.005 0.062 3162 Dihedral : 28.328 179.665 4619 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.47 % Favored : 93.12 % Rotamer: Outliers : 3.04 % Allowed : 8.61 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -3.31 (0.15), residues: 2240 helix: -1.40 (0.12), residues: 1304 sheet: -2.80 (0.32), residues: 200 loop : -3.28 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.007 0.001 HIS C 412 PHE 0.023 0.002 PHE D 541 TYR 0.018 0.002 TYR C 702 ARG 0.007 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 314 time to evaluate : 2.111 Fit side-chains REVERT: A 503 MET cc_start: 0.8633 (ttp) cc_final: 0.8429 (ttm) REVERT: A 663 LYS cc_start: 0.8806 (mptp) cc_final: 0.8512 (mttt) REVERT: A 669 LYS cc_start: 0.7609 (ttmt) cc_final: 0.7102 (mtpt) REVERT: A 860 TYR cc_start: 0.7994 (m-80) cc_final: 0.7633 (m-80) REVERT: A 998 TYR cc_start: 0.7542 (p90) cc_final: 0.7303 (p90) REVERT: B 695 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.5916 (mptt) REVERT: C 630 VAL cc_start: 0.8642 (t) cc_final: 0.8424 (m) REVERT: C 860 TYR cc_start: 0.8069 (m-80) cc_final: 0.7777 (m-80) REVERT: C 957 ILE cc_start: 0.7989 (mm) cc_final: 0.7782 (mp) REVERT: C 998 TYR cc_start: 0.7576 (p90) cc_final: 0.7227 (p90) REVERT: D 695 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.5221 (mptt) REVERT: D 706 SER cc_start: 0.8862 (t) cc_final: 0.8594 (p) REVERT: D 770 LYS cc_start: 0.7693 (mmtp) cc_final: 0.7403 (tttp) outliers start: 59 outliers final: 30 residues processed: 356 average time/residue: 0.3153 time to fit residues: 173.7317 Evaluate side-chains 312 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 170 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20308 Z= 0.298 Angle : 1.265 34.059 27264 Z= 0.490 Chirality : 0.145 2.418 2961 Planarity : 0.004 0.052 3162 Dihedral : 27.135 179.930 4619 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.14 % Favored : 92.50 % Rotamer: Outliers : 3.71 % Allowed : 9.90 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.93 (0.17), residues: 2240 helix: -0.04 (0.14), residues: 1312 sheet: -2.73 (0.31), residues: 202 loop : -3.10 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 861 HIS 0.017 0.002 HIS C 883 PHE 0.021 0.002 PHE C 495 TYR 0.018 0.002 TYR C 702 ARG 0.007 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 305 time to evaluate : 2.138 Fit side-chains REVERT: A 503 MET cc_start: 0.8745 (ttp) cc_final: 0.8536 (ttm) REVERT: A 511 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8137 (tptp) REVERT: A 663 LYS cc_start: 0.8809 (mptp) cc_final: 0.8525 (mttt) REVERT: A 669 LYS cc_start: 0.7643 (ttmt) cc_final: 0.7134 (mtpt) REVERT: A 860 TYR cc_start: 0.7984 (m-80) cc_final: 0.7555 (m-80) REVERT: A 952 ARG cc_start: 0.6968 (ptp-170) cc_final: 0.6594 (ptp-170) REVERT: A 985 ASN cc_start: 0.7848 (m-40) cc_final: 0.7620 (m110) REVERT: B 695 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6206 (mptt) REVERT: B 715 ARG cc_start: 0.7674 (mmt-90) cc_final: 0.7367 (mmt-90) REVERT: B 721 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.8002 (ttp) REVERT: C 585 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7423 (mmt) REVERT: C 630 VAL cc_start: 0.8588 (t) cc_final: 0.8310 (m) REVERT: C 860 TYR cc_start: 0.8093 (m-80) cc_final: 0.7661 (m-80) REVERT: C 998 TYR cc_start: 0.7848 (p90) cc_final: 0.7407 (p90) REVERT: D 414 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (ptp) REVERT: D 461 ASN cc_start: 0.7350 (t0) cc_final: 0.7014 (t0) REVERT: D 695 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5770 (mptt) REVERT: D 715 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7609 (mmt-90) REVERT: D 770 LYS cc_start: 0.7669 (mmtp) cc_final: 0.7372 (tttp) REVERT: E 10 TYR cc_start: 0.8642 (m-80) cc_final: 0.8345 (m-80) outliers start: 72 outliers final: 45 residues processed: 357 average time/residue: 0.3105 time to fit residues: 171.4540 Evaluate side-chains 330 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN C 990 ASN D 508 GLN F 75 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20308 Z= 0.315 Angle : 1.243 33.135 27264 Z= 0.480 Chirality : 0.144 2.355 2961 Planarity : 0.004 0.042 3162 Dihedral : 26.504 179.968 4619 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.37 % Favored : 92.28 % Rotamer: Outliers : 4.18 % Allowed : 10.62 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.17), residues: 2240 helix: 0.60 (0.14), residues: 1314 sheet: -2.64 (0.32), residues: 192 loop : -2.96 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 766 HIS 0.012 0.002 HIS C 883 PHE 0.018 0.002 PHE B 438 TYR 0.027 0.002 TYR C 980 ARG 0.006 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 287 time to evaluate : 2.121 Fit side-chains revert: symmetry clash REVERT: A 587 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.6605 (mm-40) REVERT: A 647 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: A 663 LYS cc_start: 0.8863 (mptp) cc_final: 0.8567 (mttt) REVERT: A 669 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7160 (mtpt) REVERT: A 697 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8073 (pttp) REVERT: A 860 TYR cc_start: 0.8036 (m-80) cc_final: 0.7609 (m-80) REVERT: A 952 ARG cc_start: 0.6974 (ptp-170) cc_final: 0.6616 (ptp-170) REVERT: B 461 ASN cc_start: 0.7289 (t0) cc_final: 0.6886 (t0) REVERT: B 695 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6286 (mptt) REVERT: B 721 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7972 (ttp) REVERT: C 585 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7316 (mmt) REVERT: C 630 VAL cc_start: 0.8660 (t) cc_final: 0.8376 (m) REVERT: C 860 TYR cc_start: 0.8107 (m-80) cc_final: 0.7654 (m-80) REVERT: C 987 GLU cc_start: 0.6982 (tp30) cc_final: 0.6691 (tp30) REVERT: D 414 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7982 (ptp) REVERT: D 415 LEU cc_start: 0.7919 (mt) cc_final: 0.7703 (mt) REVERT: D 461 ASN cc_start: 0.7269 (t0) cc_final: 0.6838 (t0) REVERT: D 527 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: D 695 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.5868 (mptt) REVERT: D 764 ASN cc_start: 0.8073 (m110) cc_final: 0.7575 (m-40) REVERT: D 770 LYS cc_start: 0.7743 (mmtp) cc_final: 0.7413 (tttp) REVERT: D 817 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7453 (ttpt) REVERT: E 148 TYR cc_start: 0.8333 (t80) cc_final: 0.7972 (t80) REVERT: F 100 TYR cc_start: 0.8377 (t80) cc_final: 0.8088 (t80) outliers start: 81 outliers final: 52 residues processed: 348 average time/residue: 0.3088 time to fit residues: 165.5987 Evaluate side-chains 336 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 275 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 627 GLU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 0.0870 chunk 186 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS C 764 ASN ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 ASN D 508 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20308 Z= 0.179 Angle : 1.209 33.006 27264 Z= 0.458 Chirality : 0.142 2.296 2961 Planarity : 0.004 0.036 3162 Dihedral : 26.006 179.819 4619 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.83 % Favored : 92.81 % Rotamer: Outliers : 3.51 % Allowed : 12.37 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.56 (0.18), residues: 2240 helix: 1.18 (0.15), residues: 1314 sheet: -2.40 (0.33), residues: 192 loop : -2.75 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 460 HIS 0.010 0.002 HIS A 883 PHE 0.018 0.001 PHE B 438 TYR 0.026 0.001 TYR C 980 ARG 0.005 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 305 time to evaluate : 2.145 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8441 (mtm) cc_final: 0.8231 (mtp) REVERT: A 511 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8110 (tptp) REVERT: A 585 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7446 (mmt) REVERT: A 587 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.6574 (mm-40) REVERT: A 663 LYS cc_start: 0.8844 (mptp) cc_final: 0.8541 (mttt) REVERT: A 669 LYS cc_start: 0.7641 (ttmt) cc_final: 0.7146 (mtpt) REVERT: A 697 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7924 (pttp) REVERT: A 860 TYR cc_start: 0.8040 (m-80) cc_final: 0.7594 (m-80) REVERT: A 952 ARG cc_start: 0.7014 (ptp-170) cc_final: 0.6651 (ptp-170) REVERT: B 461 ASN cc_start: 0.7256 (t0) cc_final: 0.6812 (t0) REVERT: B 695 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6158 (mptt) REVERT: B 715 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7436 (mmt-90) REVERT: B 721 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7964 (ttp) REVERT: C 585 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7311 (mmt) REVERT: C 651 ASP cc_start: 0.6991 (t70) cc_final: 0.6772 (t70) REVERT: C 663 LYS cc_start: 0.8846 (mttp) cc_final: 0.8459 (mttt) REVERT: C 721 MET cc_start: 0.8631 (ptt) cc_final: 0.8410 (ptt) REVERT: C 860 TYR cc_start: 0.8112 (m-80) cc_final: 0.7883 (m-80) REVERT: C 877 GLU cc_start: 0.8192 (tt0) cc_final: 0.7730 (tt0) REVERT: C 952 ARG cc_start: 0.6983 (ptp-170) cc_final: 0.6666 (ptp-170) REVERT: C 987 GLU cc_start: 0.6992 (tp30) cc_final: 0.6711 (tp30) REVERT: D 414 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7916 (ptp) REVERT: D 415 LEU cc_start: 0.7929 (mt) cc_final: 0.7689 (mt) REVERT: D 461 ASN cc_start: 0.7224 (t0) cc_final: 0.6672 (t0) REVERT: D 695 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.5809 (mptt) REVERT: D 764 ASN cc_start: 0.8006 (m110) cc_final: 0.7523 (m-40) REVERT: D 770 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7405 (tttp) REVERT: E 148 TYR cc_start: 0.8318 (t80) cc_final: 0.7998 (t80) REVERT: F 64 LEU cc_start: 0.7906 (mm) cc_final: 0.7596 (mt) outliers start: 68 outliers final: 42 residues processed: 352 average time/residue: 0.3165 time to fit residues: 173.5299 Evaluate side-chains 337 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 287 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 773 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 764 ASN ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20308 Z= 0.266 Angle : 1.226 32.851 27264 Z= 0.468 Chirality : 0.142 2.276 2961 Planarity : 0.004 0.054 3162 Dihedral : 25.712 179.898 4619 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.10 % Favored : 92.54 % Rotamer: Outliers : 4.12 % Allowed : 11.49 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2240 helix: 1.30 (0.15), residues: 1312 sheet: -2.33 (0.33), residues: 192 loop : -2.70 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 766 HIS 0.010 0.002 HIS A 412 PHE 0.017 0.002 PHE B 438 TYR 0.025 0.002 TYR C 980 ARG 0.006 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 303 time to evaluate : 2.243 Fit side-chains revert: symmetry clash REVERT: A 503 MET cc_start: 0.8807 (ttp) cc_final: 0.8544 (ttm) REVERT: A 585 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7555 (mmt) REVERT: A 587 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6611 (mm-40) REVERT: A 663 LYS cc_start: 0.8854 (mptp) cc_final: 0.8552 (mttt) REVERT: A 669 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7089 (mtpt) REVERT: A 697 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7956 (pttp) REVERT: A 755 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7909 (mt-10) REVERT: A 860 TYR cc_start: 0.8023 (m-80) cc_final: 0.7549 (m-80) REVERT: A 877 GLU cc_start: 0.8217 (tt0) cc_final: 0.7822 (tt0) REVERT: A 952 ARG cc_start: 0.7068 (ptp-170) cc_final: 0.6735 (ptp-170) REVERT: A 985 ASN cc_start: 0.7498 (m-40) cc_final: 0.7272 (m-40) REVERT: B 461 ASN cc_start: 0.7226 (t0) cc_final: 0.6770 (t0) REVERT: B 695 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6268 (mptt) REVERT: B 721 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.8012 (ttp) REVERT: B 764 ASN cc_start: 0.8114 (m110) cc_final: 0.7606 (m-40) REVERT: C 585 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7433 (mmt) REVERT: C 663 LYS cc_start: 0.8884 (mttp) cc_final: 0.8483 (mttt) REVERT: C 669 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7199 (mtpt) REVERT: C 860 TYR cc_start: 0.8123 (m-80) cc_final: 0.7915 (m-80) REVERT: C 877 GLU cc_start: 0.8201 (tt0) cc_final: 0.7744 (tt0) REVERT: C 880 MET cc_start: 0.7437 (tpp) cc_final: 0.7161 (tpp) REVERT: C 901 PHE cc_start: 0.7152 (m-10) cc_final: 0.6842 (m-10) REVERT: C 952 ARG cc_start: 0.7003 (ptp-170) cc_final: 0.6617 (ptp-170) REVERT: D 414 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7811 (ptp) REVERT: D 415 LEU cc_start: 0.7935 (mt) cc_final: 0.7726 (mt) REVERT: D 461 ASN cc_start: 0.7239 (t0) cc_final: 0.6801 (t0) REVERT: D 695 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6057 (mptt) REVERT: D 764 ASN cc_start: 0.8062 (m110) cc_final: 0.7541 (m-40) REVERT: D 770 LYS cc_start: 0.7773 (mmtp) cc_final: 0.7452 (tttp) REVERT: D 817 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7460 (ttmt) REVERT: E 100 TYR cc_start: 0.8223 (t80) cc_final: 0.8003 (t80) REVERT: E 148 TYR cc_start: 0.8306 (t80) cc_final: 0.7976 (t80) REVERT: F 64 LEU cc_start: 0.8044 (mm) cc_final: 0.7719 (mt) outliers start: 80 outliers final: 57 residues processed: 361 average time/residue: 0.3107 time to fit residues: 173.2499 Evaluate side-chains 357 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 292 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 902 THR Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20308 Z= 0.210 Angle : 1.213 32.833 27264 Z= 0.460 Chirality : 0.142 2.269 2961 Planarity : 0.004 0.046 3162 Dihedral : 25.500 179.943 4619 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.23 % Favored : 92.41 % Rotamer: Outliers : 3.71 % Allowed : 12.53 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2240 helix: 1.50 (0.15), residues: 1306 sheet: -2.21 (0.33), residues: 192 loop : -2.62 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 766 HIS 0.016 0.002 HIS C 412 PHE 0.032 0.001 PHE B 515 TYR 0.026 0.001 TYR C 980 ARG 0.006 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 307 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: A 503 MET cc_start: 0.8849 (ttp) cc_final: 0.8552 (ttm) REVERT: A 585 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7500 (mmt) REVERT: A 587 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6561 (mm-40) REVERT: A 647 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: A 663 LYS cc_start: 0.8852 (mptp) cc_final: 0.8551 (mttt) REVERT: A 669 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7104 (mtpt) REVERT: A 684 ARG cc_start: 0.8196 (ttm110) cc_final: 0.7983 (ttm110) REVERT: A 697 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7971 (pttp) REVERT: A 755 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 860 TYR cc_start: 0.8039 (m-80) cc_final: 0.7600 (m-80) REVERT: A 877 GLU cc_start: 0.8211 (tt0) cc_final: 0.7821 (tt0) REVERT: A 952 ARG cc_start: 0.7068 (ptp-170) cc_final: 0.6730 (ptp-170) REVERT: A 985 ASN cc_start: 0.7372 (m-40) cc_final: 0.7132 (m110) REVERT: B 461 ASN cc_start: 0.7175 (t0) cc_final: 0.6783 (t0) REVERT: B 695 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6700 (tmtt) REVERT: B 715 ARG cc_start: 0.7694 (mmt-90) cc_final: 0.7449 (mmt-90) REVERT: B 721 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: B 764 ASN cc_start: 0.8122 (m110) cc_final: 0.7607 (m-40) REVERT: C 585 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7356 (mmt) REVERT: C 663 LYS cc_start: 0.8880 (mttp) cc_final: 0.8481 (mttt) REVERT: C 669 LYS cc_start: 0.7694 (ttmt) cc_final: 0.7181 (mtpt) REVERT: C 877 GLU cc_start: 0.8191 (tt0) cc_final: 0.7736 (tt0) REVERT: C 880 MET cc_start: 0.7398 (tpp) cc_final: 0.7183 (tpp) REVERT: C 901 PHE cc_start: 0.7105 (m-10) cc_final: 0.6814 (m-10) REVERT: C 952 ARG cc_start: 0.6990 (ptp-170) cc_final: 0.6590 (ptp-170) REVERT: D 414 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7790 (ptp) REVERT: D 461 ASN cc_start: 0.7159 (t0) cc_final: 0.6707 (t0) REVERT: D 695 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6048 (mptt) REVERT: D 715 ARG cc_start: 0.7701 (mmt-90) cc_final: 0.7274 (mmt-90) REVERT: D 764 ASN cc_start: 0.8088 (m110) cc_final: 0.7593 (m-40) REVERT: D 770 LYS cc_start: 0.7762 (mmtp) cc_final: 0.7396 (tttp) REVERT: D 817 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7376 (ttmt) REVERT: E 148 TYR cc_start: 0.8309 (t80) cc_final: 0.7984 (t80) REVERT: F 64 LEU cc_start: 0.8019 (mm) cc_final: 0.7672 (mt) outliers start: 72 outliers final: 52 residues processed: 352 average time/residue: 0.3176 time to fit residues: 173.1630 Evaluate side-chains 355 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20308 Z= 0.239 Angle : 1.218 32.732 27264 Z= 0.464 Chirality : 0.142 2.261 2961 Planarity : 0.004 0.060 3162 Dihedral : 25.372 179.966 4619 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.19 % Favored : 92.46 % Rotamer: Outliers : 3.81 % Allowed : 12.84 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2240 helix: 1.50 (0.15), residues: 1306 sheet: -2.14 (0.33), residues: 192 loop : -2.60 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.023 0.002 HIS A 412 PHE 0.019 0.001 PHE B 438 TYR 0.027 0.001 TYR C 980 ARG 0.008 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 290 time to evaluate : 2.069 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8477 (mtm) cc_final: 0.8264 (mtp) REVERT: A 585 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7516 (mmt) REVERT: A 587 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.6586 (mm-40) REVERT: A 647 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7477 (m-10) REVERT: A 663 LYS cc_start: 0.8856 (mptp) cc_final: 0.8553 (mttt) REVERT: A 669 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7104 (mtpt) REVERT: A 684 ARG cc_start: 0.8214 (ttm110) cc_final: 0.8006 (ttm110) REVERT: A 697 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7958 (pttp) REVERT: A 709 ASN cc_start: 0.8712 (t0) cc_final: 0.8389 (t0) REVERT: A 755 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 859 ASP cc_start: 0.7726 (p0) cc_final: 0.7332 (p0) REVERT: A 877 GLU cc_start: 0.8213 (tt0) cc_final: 0.7833 (tt0) REVERT: A 952 ARG cc_start: 0.7128 (ptp-170) cc_final: 0.6789 (ptp-170) REVERT: B 461 ASN cc_start: 0.7122 (t0) cc_final: 0.6750 (t0) REVERT: B 635 SER cc_start: 0.8763 (t) cc_final: 0.8341 (p) REVERT: B 695 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6723 (tmtt) REVERT: B 715 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7443 (mmt-90) REVERT: B 721 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.8019 (ttp) REVERT: B 764 ASN cc_start: 0.8122 (m110) cc_final: 0.7616 (m-40) REVERT: C 407 MET cc_start: 0.8495 (mtm) cc_final: 0.8289 (mtp) REVERT: C 585 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7391 (mmt) REVERT: C 663 LYS cc_start: 0.8880 (mttp) cc_final: 0.8489 (mttt) REVERT: C 669 LYS cc_start: 0.7715 (ttmt) cc_final: 0.7181 (mtpt) REVERT: C 859 ASP cc_start: 0.7673 (p0) cc_final: 0.7375 (p0) REVERT: C 877 GLU cc_start: 0.8192 (tt0) cc_final: 0.7743 (tt0) REVERT: C 901 PHE cc_start: 0.7153 (m-10) cc_final: 0.6821 (m-10) REVERT: C 952 ARG cc_start: 0.7013 (ptp-170) cc_final: 0.6690 (ptp-170) REVERT: D 461 ASN cc_start: 0.7154 (t0) cc_final: 0.6751 (t0) REVERT: D 695 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6084 (mptt) REVERT: D 764 ASN cc_start: 0.8101 (m110) cc_final: 0.7608 (m-40) REVERT: D 770 LYS cc_start: 0.7791 (mmtp) cc_final: 0.7479 (tttp) REVERT: D 817 LYS cc_start: 0.7661 (ttmt) cc_final: 0.7389 (ttmt) REVERT: E 148 TYR cc_start: 0.8314 (t80) cc_final: 0.7997 (t80) REVERT: F 64 LEU cc_start: 0.8058 (mm) cc_final: 0.7696 (mt) outliers start: 74 outliers final: 57 residues processed: 339 average time/residue: 0.3160 time to fit residues: 164.9291 Evaluate side-chains 353 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 9.9990 chunk 190 optimal weight: 0.3980 chunk 202 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 191 optimal weight: 0.4980 chunk 133 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20308 Z= 0.358 Angle : 1.249 33.038 27264 Z= 0.482 Chirality : 0.142 2.298 2961 Planarity : 0.004 0.059 3162 Dihedral : 25.402 179.677 4619 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.68 % Favored : 91.96 % Rotamer: Outliers : 3.66 % Allowed : 13.35 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2240 helix: 1.32 (0.14), residues: 1312 sheet: -2.17 (0.33), residues: 192 loop : -2.68 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 766 HIS 0.015 0.002 HIS C 412 PHE 0.020 0.002 PHE B 438 TYR 0.027 0.002 TYR C 980 ARG 0.008 0.000 ARG C 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 281 time to evaluate : 2.194 Fit side-chains REVERT: A 585 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7565 (mmt) REVERT: A 587 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.6625 (mm-40) REVERT: A 647 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: A 663 LYS cc_start: 0.8860 (mptp) cc_final: 0.8546 (mttt) REVERT: A 669 LYS cc_start: 0.7709 (ttmt) cc_final: 0.7041 (mtpt) REVERT: A 684 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8095 (ttm110) REVERT: A 697 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7958 (pttp) REVERT: A 859 ASP cc_start: 0.7800 (p0) cc_final: 0.7313 (p0) REVERT: A 860 TYR cc_start: 0.8042 (m-80) cc_final: 0.7558 (m-80) REVERT: A 877 GLU cc_start: 0.8226 (tt0) cc_final: 0.7826 (tt0) REVERT: A 952 ARG cc_start: 0.7118 (ptp-170) cc_final: 0.6785 (ptp-170) REVERT: B 461 ASN cc_start: 0.7159 (t0) cc_final: 0.6816 (t0) REVERT: B 695 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6886 (tmtt) REVERT: B 715 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7481 (mmt-90) REVERT: B 721 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8026 (ttp) REVERT: B 764 ASN cc_start: 0.8145 (m110) cc_final: 0.7625 (m-40) REVERT: C 585 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7411 (mmt) REVERT: C 663 LYS cc_start: 0.8887 (mttp) cc_final: 0.8502 (mttt) REVERT: C 669 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7166 (mtpt) REVERT: C 709 ASN cc_start: 0.8763 (t0) cc_final: 0.8536 (t0) REVERT: C 859 ASP cc_start: 0.7704 (p0) cc_final: 0.7385 (p0) REVERT: C 877 GLU cc_start: 0.8168 (tt0) cc_final: 0.7775 (tt0) REVERT: C 901 PHE cc_start: 0.7180 (m-10) cc_final: 0.6875 (m-10) REVERT: C 952 ARG cc_start: 0.7043 (ptp-170) cc_final: 0.6708 (ptp-170) REVERT: D 461 ASN cc_start: 0.7154 (t0) cc_final: 0.6813 (t0) REVERT: D 695 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6703 (tmtt) REVERT: D 764 ASN cc_start: 0.8128 (m110) cc_final: 0.7608 (m-40) REVERT: D 770 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7528 (tttp) REVERT: D 817 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7390 (ttmt) REVERT: E 148 TYR cc_start: 0.8321 (t80) cc_final: 0.7945 (t80) REVERT: F 64 LEU cc_start: 0.8089 (mm) cc_final: 0.7726 (mt) outliers start: 71 outliers final: 56 residues processed: 335 average time/residue: 0.3211 time to fit residues: 165.2380 Evaluate side-chains 344 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 280 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 719 ASP Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 138 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 190 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20308 Z= 0.200 Angle : 1.217 32.906 27264 Z= 0.463 Chirality : 0.142 2.272 2961 Planarity : 0.004 0.054 3162 Dihedral : 25.220 179.806 4619 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.32 % Favored : 92.32 % Rotamer: Outliers : 3.20 % Allowed : 13.76 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2240 helix: 1.53 (0.15), residues: 1308 sheet: -2.03 (0.34), residues: 192 loop : -2.57 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.021 0.002 HIS A 412 PHE 0.021 0.001 PHE B 438 TYR 0.027 0.001 TYR C 980 ARG 0.008 0.000 ARG C 684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 283 time to evaluate : 2.220 Fit side-chains REVERT: A 585 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7492 (mmt) REVERT: A 587 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.6593 (mm-40) REVERT: A 647 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7520 (m-10) REVERT: A 663 LYS cc_start: 0.8859 (mptp) cc_final: 0.8542 (mttt) REVERT: A 669 LYS cc_start: 0.7700 (ttmt) cc_final: 0.7100 (mtpt) REVERT: A 684 ARG cc_start: 0.8294 (ttm110) cc_final: 0.8086 (ttm110) REVERT: A 697 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7930 (pttp) REVERT: A 859 ASP cc_start: 0.7725 (p0) cc_final: 0.7254 (p0) REVERT: A 860 TYR cc_start: 0.8065 (m-80) cc_final: 0.7591 (m-80) REVERT: A 877 GLU cc_start: 0.8191 (tt0) cc_final: 0.7798 (tt0) REVERT: A 952 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6800 (ptp-170) REVERT: B 461 ASN cc_start: 0.7128 (t0) cc_final: 0.6793 (t0) REVERT: B 695 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6247 (mptt) REVERT: B 715 ARG cc_start: 0.7736 (mmt-90) cc_final: 0.7476 (mmt-90) REVERT: B 721 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: B 764 ASN cc_start: 0.8130 (m110) cc_final: 0.7602 (m-40) REVERT: C 585 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7369 (mmt) REVERT: C 663 LYS cc_start: 0.8875 (mttp) cc_final: 0.8497 (mttt) REVERT: C 669 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7181 (mtpt) REVERT: C 859 ASP cc_start: 0.7678 (p0) cc_final: 0.7316 (p0) REVERT: C 860 TYR cc_start: 0.7971 (m-80) cc_final: 0.7729 (m-80) REVERT: C 877 GLU cc_start: 0.8159 (tt0) cc_final: 0.7722 (tt0) REVERT: C 901 PHE cc_start: 0.7182 (m-10) cc_final: 0.6871 (m-10) REVERT: C 952 ARG cc_start: 0.7039 (ptp-170) cc_final: 0.6709 (ptp-170) REVERT: C 986 ASP cc_start: 0.6821 (p0) cc_final: 0.6536 (p0) REVERT: D 461 ASN cc_start: 0.7098 (t0) cc_final: 0.6760 (t0) REVERT: D 695 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6059 (mptt) REVERT: D 715 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7609 (mmt-90) REVERT: D 764 ASN cc_start: 0.8084 (m110) cc_final: 0.7578 (m-40) REVERT: D 770 LYS cc_start: 0.7791 (mmtp) cc_final: 0.7483 (tttp) REVERT: D 817 LYS cc_start: 0.7669 (ttmt) cc_final: 0.7392 (ttmt) REVERT: E 148 TYR cc_start: 0.8319 (t80) cc_final: 0.8021 (t80) REVERT: F 64 LEU cc_start: 0.8085 (mm) cc_final: 0.7725 (mt) outliers start: 62 outliers final: 47 residues processed: 324 average time/residue: 0.3240 time to fit residues: 161.5709 Evaluate side-chains 332 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 277 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 412 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 585 MET Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 719 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 524 GLU Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 706 SER Chi-restraints excluded: chain C residue 719 ASP Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 957 ILE Chi-restraints excluded: chain C residue 1013 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 123 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS ** A 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.168964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121670 restraints weight = 21968.587| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.25 r_work: 0.3008 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20308 Z= 0.349 Angle : 1.246 33.040 27264 Z= 0.480 Chirality : 0.142 2.294 2961 Planarity : 0.004 0.061 3162 Dihedral : 25.232 179.869 4619 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.63 % Favored : 92.05 % Rotamer: Outliers : 3.40 % Allowed : 13.71 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2240 helix: 1.38 (0.14), residues: 1312 sheet: -2.06 (0.33), residues: 192 loop : -2.64 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 766 HIS 0.017 0.002 HIS A 412 PHE 0.021 0.002 PHE B 438 TYR 0.027 0.002 TYR C 980 ARG 0.008 0.000 ARG C 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.74 seconds wall clock time: 85 minutes 51.02 seconds (5151.02 seconds total)