Starting phenix.real_space_refine on Mon Mar 18 09:36:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/03_2024/6pqp_20450_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 152 5.16 5 C 13524 2.51 5 N 3216 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D GLU 966": "OE1" <-> "OE2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D ARG 996": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B GLU 966": "OE1" <-> "OE2" Residue "B ARG 975": "NH1" <-> "NH2" Residue "B ARG 996": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 694": "NH1" <-> "NH2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C GLU 966": "OE1" <-> "OE2" Residue "C ARG 975": "NH1" <-> "NH2" Residue "C ARG 996": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4854 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 21, 'TRANS': 593} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 200 Unusual residues: {'6OU': 4, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'6OU': 5, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 282 Unusual residues: {'6OU': 6, '9BE': 1, 'LBN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'6OU:plan-1': 3} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 9.72, per 1000 atoms: 0.47 Number of scatterers: 20492 At special positions: 0 Unit cell: (111.93, 111.93, 148.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 24 15.00 O 3576 8.00 N 3216 7.00 C 13524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN D 747 " " NAG G 1 " - " ASN B 747 " " NAG H 1 " - " ASN C 747 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 2.8 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 4 sheets defined 63.3% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.06 Creating SS restraints... Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 551 through 557 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 631 through 641 removed outlier: 4.058A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 670 No H-bonds generated for 'chain 'A' and resid 667 through 670' Processing helix chain 'A' and resid 673 through 676 No H-bonds generated for 'chain 'A' and resid 673 through 676' Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 713 Processing helix chain 'A' and resid 715 through 738 removed outlier: 3.801A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 795 removed outlier: 3.586A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 822 removed outlier: 3.540A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.687A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 850 " --> pdb=" O PHE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 872 Processing helix chain 'A' and resid 874 through 891 Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.888A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 986 removed outlier: 4.076A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1017 through 1023 Processing helix chain 'A' and resid 1040 through 1071 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 485 through 491 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 536 Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 593 through 600 Processing helix chain 'D' and resid 605 through 610 Processing helix chain 'D' and resid 622 through 629 Processing helix chain 'D' and resid 631 through 641 removed outlier: 4.058A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 670 No H-bonds generated for 'chain 'D' and resid 667 through 670' Processing helix chain 'D' and resid 673 through 676 No H-bonds generated for 'chain 'D' and resid 673 through 676' Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 713 Processing helix chain 'D' and resid 715 through 738 removed outlier: 3.802A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 795 removed outlier: 3.586A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 822 removed outlier: 3.541A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Proline residue: D 821 - end of helix Processing helix chain 'D' and resid 828 through 850 removed outlier: 3.687A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 850 " --> pdb=" O PHE D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 872 Processing helix chain 'D' and resid 874 through 891 Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.888A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 927 Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 986 removed outlier: 4.076A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1017 through 1023 Processing helix chain 'D' and resid 1040 through 1071 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 485 through 491 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 551 through 557 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 631 through 641 removed outlier: 4.058A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 670 No H-bonds generated for 'chain 'B' and resid 667 through 670' Processing helix chain 'B' and resid 673 through 676 No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 713 Processing helix chain 'B' and resid 715 through 738 removed outlier: 3.802A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 795 removed outlier: 3.586A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 822 removed outlier: 3.540A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Proline residue: B 821 - end of helix Processing helix chain 'B' and resid 828 through 850 removed outlier: 3.687A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 850 " --> pdb=" O PHE B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 872 Processing helix chain 'B' and resid 874 through 891 Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.888A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 986 removed outlier: 4.076A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1017 through 1023 Processing helix chain 'B' and resid 1040 through 1071 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 536 Processing helix chain 'C' and resid 551 through 557 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 593 through 600 Processing helix chain 'C' and resid 605 through 610 Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 631 through 641 removed outlier: 4.058A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 670 No H-bonds generated for 'chain 'C' and resid 667 through 670' Processing helix chain 'C' and resid 673 through 676 No H-bonds generated for 'chain 'C' and resid 673 through 676' Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 713 Processing helix chain 'C' and resid 715 through 738 removed outlier: 3.801A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 795 removed outlier: 3.587A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 822 removed outlier: 3.540A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Proline residue: C 821 - end of helix Processing helix chain 'C' and resid 828 through 850 removed outlier: 3.686A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 850 " --> pdb=" O PHE C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 872 Processing helix chain 'C' and resid 874 through 891 Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.889A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 986 removed outlier: 4.076A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1017 through 1023 Processing helix chain 'C' and resid 1040 through 1071 Processing sheet with id= A, first strand: chain 'A' and resid 656 through 659 Processing sheet with id= B, first strand: chain 'D' and resid 656 through 659 Processing sheet with id= C, first strand: chain 'B' and resid 656 through 659 Processing sheet with id= D, first strand: chain 'C' and resid 656 through 659 960 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3064 1.30 - 1.43: 5374 1.43 - 1.56: 11947 1.56 - 1.68: 255 1.68 - 1.81: 276 Bond restraints: 20916 Sorted by residual: bond pdb=" O2 LBN C1208 " pdb=" P1 LBN C1208 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN A1206 " pdb=" P1 LBN A1206 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" O2 LBN D1205 " pdb=" P1 LBN D1205 " ideal model delta sigma weight residual 1.650 1.797 -0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O2 LBN B1207 " pdb=" P1 LBN B1207 " ideal model delta sigma weight residual 1.650 1.796 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O22 6OU B1204 " pdb=" P23 6OU B1204 " ideal model delta sigma weight residual 1.643 1.738 -0.095 2.00e-02 2.50e+03 2.26e+01 ... (remaining 20911 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.28: 424 105.28 - 112.49: 10654 112.49 - 119.70: 7561 119.70 - 126.91: 9241 126.91 - 134.12: 288 Bond angle restraints: 28168 Sorted by residual: angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.23 119.24 -11.01 1.53e+00 4.27e-01 5.18e+01 angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.23 119.22 -10.99 1.53e+00 4.27e-01 5.16e+01 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.23 119.20 -10.97 1.53e+00 4.27e-01 5.14e+01 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.23 119.17 -10.94 1.53e+00 4.27e-01 5.11e+01 angle pdb=" O22 6OU D1204 " pdb=" P23 6OU D1204 " pdb=" O26 6OU D1204 " ideal model delta sigma weight residual 93.95 109.29 -15.34 3.00e+00 1.11e-01 2.61e+01 ... (remaining 28163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 12192 34.20 - 68.39: 420 68.39 - 102.59: 136 102.59 - 136.78: 32 136.78 - 170.98: 32 Dihedral angle restraints: 12812 sinusoidal: 5568 harmonic: 7244 Sorted by residual: dihedral pdb=" C1 LBN C1208 " pdb=" O1 LBN C1208 " pdb=" P1 LBN C1208 " pdb=" O3 LBN C1208 " ideal model delta sinusoidal sigma weight residual 275.40 104.42 170.98 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN D1205 " pdb=" O1 LBN D1205 " pdb=" P1 LBN D1205 " pdb=" O3 LBN D1205 " ideal model delta sinusoidal sigma weight residual 275.40 104.45 170.95 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C1 LBN A1206 " pdb=" O1 LBN A1206 " pdb=" P1 LBN A1206 " pdb=" O3 LBN A1206 " ideal model delta sinusoidal sigma weight residual 275.40 104.46 170.94 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 3220 1.215 - 2.431: 0 2.431 - 3.646: 0 3.646 - 4.861: 0 4.861 - 6.076: 4 Chirality restraints: 3224 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 747 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 747 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 3.68 -6.08 2.00e-01 2.50e+01 9.23e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 747 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 3.67 -6.07 2.00e-01 2.50e+01 9.23e+02 ... (remaining 3221 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG H 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.234 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG E 2 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.234 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" C7 NAG F 2 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.322 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 355 2.69 - 3.24: 18625 3.24 - 3.79: 30684 3.79 - 4.35: 40903 4.35 - 4.90: 66611 Nonbonded interactions: 157178 Sorted by model distance: nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.132 2.520 nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.132 2.520 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.132 2.520 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.132 2.520 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.284 2.440 ... (remaining 157173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'B' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) selection = (chain 'C' and (resid 446 through 1079 or resid 1204)) selection = (chain 'D' and (resid 446 through 1079 or (resid 1204 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C19 or name \ C20 or name C21 or name C31 or name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name O17 or name O18 or name O22 \ or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.760 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 49.840 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.170 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.147 20916 Z= 0.772 Angle : 1.292 15.338 28168 Z= 0.588 Chirality : 0.226 6.076 3224 Planarity : 0.011 0.195 3392 Dihedral : 21.817 170.977 8108 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.19 % Allowed : 4.80 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.14), residues: 2436 helix: -2.21 (0.09), residues: 1756 sheet: 1.02 (0.80), residues: 68 loop : -1.74 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 515 HIS 0.011 0.003 HIS C 494 PHE 0.035 0.004 PHE D 888 TYR 0.042 0.003 TYR C 785 ARG 0.016 0.001 ARG D 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 614 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8313 (mm-30) REVERT: A 720 MET cc_start: 0.7790 (mmm) cc_final: 0.7513 (mmm) REVERT: A 826 ILE cc_start: 0.8749 (mt) cc_final: 0.8521 (tt) REVERT: A 930 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 1042 MET cc_start: 0.7688 (ppp) cc_final: 0.7398 (ptt) REVERT: D 571 ASN cc_start: 0.8297 (m110) cc_final: 0.7993 (t0) REVERT: D 783 PHE cc_start: 0.8045 (m-80) cc_final: 0.7789 (m-10) REVERT: D 981 GLU cc_start: 0.8048 (tp30) cc_final: 0.7732 (mm-30) REVERT: D 986 LEU cc_start: 0.9266 (tt) cc_final: 0.8922 (tt) REVERT: D 1077 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 591 LYS cc_start: 0.9374 (mttt) cc_final: 0.9169 (mtmm) REVERT: B 643 LEU cc_start: 0.7727 (mp) cc_final: 0.7336 (mp) REVERT: B 1075 ILE cc_start: 0.7807 (mt) cc_final: 0.7077 (mm) REVERT: C 770 ILE cc_start: 0.9317 (mt) cc_final: 0.9084 (mm) REVERT: C 981 GLU cc_start: 0.7936 (tp30) cc_final: 0.7619 (tp30) REVERT: C 985 SER cc_start: 0.9199 (t) cc_final: 0.8779 (p) REVERT: C 1075 ILE cc_start: 0.8628 (mt) cc_final: 0.8006 (mm) outliers start: 4 outliers final: 3 residues processed: 614 average time/residue: 0.3338 time to fit residues: 311.8223 Evaluate side-chains 308 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 0.0970 chunk 221 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 549 ASN A 570 HIS A 644 HIS A 700 HIS A 739 ASN A 805 ASN A 893 ASN A 983 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 460 ASN D 476 ASN D 512 HIS D 519 HIS D 549 ASN D 570 HIS D 577 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN D 893 ASN D 983 HIS ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 460 ASN B 476 ASN B 512 HIS B 519 HIS ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 983 HIS ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 476 ASN C 494 HIS C 512 HIS C 519 HIS C 537 ASN C 549 ASN C 644 HIS C 692 ASN C 700 HIS C 719 HIS C 805 ASN C 893 ASN C 907 GLN C 970 HIS C 983 HIS C1047 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20916 Z= 0.198 Angle : 0.652 9.081 28168 Z= 0.303 Chirality : 0.044 0.282 3224 Planarity : 0.004 0.061 3392 Dihedral : 23.029 155.347 3606 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.74 % Allowed : 11.56 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2436 helix: -0.34 (0.12), residues: 1720 sheet: 4.08 (0.86), residues: 48 loop : -1.11 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 515 HIS 0.005 0.001 HIS A 970 PHE 0.013 0.001 PHE D 823 TYR 0.014 0.001 TYR D 768 ARG 0.005 0.001 ARG D 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 343 time to evaluate : 2.284 Fit side-chains REVERT: A 483 MET cc_start: 0.8193 (mtt) cc_final: 0.7670 (mtp) REVERT: A 625 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 721 MET cc_start: 0.7896 (tpp) cc_final: 0.7666 (mmp) REVERT: A 1042 MET cc_start: 0.7577 (ppp) cc_final: 0.7322 (ptt) REVERT: D 607 GLU cc_start: 0.7950 (mp0) cc_final: 0.7708 (mp0) REVERT: D 768 TYR cc_start: 0.7355 (p90) cc_final: 0.7132 (p90) REVERT: D 981 GLU cc_start: 0.8102 (tp30) cc_final: 0.7711 (tp30) REVERT: D 985 SER cc_start: 0.9326 (t) cc_final: 0.8580 (p) REVERT: B 488 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8471 (mm) REVERT: B 985 SER cc_start: 0.9282 (t) cc_final: 0.9012 (p) REVERT: B 1024 PHE cc_start: 0.9050 (m-80) cc_final: 0.8729 (m-80) REVERT: B 1073 GLU cc_start: 0.7251 (tt0) cc_final: 0.6902 (tt0) REVERT: B 1075 ILE cc_start: 0.8351 (mt) cc_final: 0.8069 (mm) REVERT: C 770 ILE cc_start: 0.9438 (mt) cc_final: 0.9214 (mm) REVERT: C 981 GLU cc_start: 0.8028 (tp30) cc_final: 0.7630 (tp30) REVERT: C 985 SER cc_start: 0.9183 (t) cc_final: 0.8546 (p) REVERT: C 998 VAL cc_start: 0.9008 (p) cc_final: 0.8745 (m) REVERT: C 1075 ILE cc_start: 0.8660 (mt) cc_final: 0.8329 (mp) outliers start: 57 outliers final: 19 residues processed: 380 average time/residue: 0.2803 time to fit residues: 169.3316 Evaluate side-chains 299 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 775 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 933 HIS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 197 optimal weight: 0.0870 chunk 220 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 HIS D 560 HIS D 590 ASN D 907 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 ASN C1047 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20916 Z= 0.199 Angle : 0.592 8.629 28168 Z= 0.279 Chirality : 0.041 0.220 3224 Planarity : 0.004 0.056 3392 Dihedral : 21.192 149.277 3600 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.07 % Allowed : 12.38 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2436 helix: 0.47 (0.12), residues: 1744 sheet: 4.31 (0.88), residues: 48 loop : -0.69 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 515 HIS 0.005 0.001 HIS D 494 PHE 0.013 0.001 PHE B1020 TYR 0.022 0.001 TYR C 768 ARG 0.004 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 311 time to evaluate : 2.441 Fit side-chains REVERT: A 681 GLU cc_start: 0.7918 (pm20) cc_final: 0.7690 (pm20) REVERT: A 721 MET cc_start: 0.7831 (tpp) cc_final: 0.7599 (mmp) REVERT: A 891 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8888 (mp) REVERT: D 852 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7135 (mmm-85) REVERT: D 981 GLU cc_start: 0.8122 (tp30) cc_final: 0.7903 (tp30) REVERT: D 985 SER cc_start: 0.9319 (t) cc_final: 0.8851 (p) REVERT: B 709 MET cc_start: 0.9036 (tmm) cc_final: 0.8776 (tmm) REVERT: B 785 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7196 (m-10) REVERT: B 852 ARG cc_start: 0.7546 (mmm-85) cc_final: 0.7195 (mmm-85) REVERT: B 946 ILE cc_start: 0.9379 (mm) cc_final: 0.9156 (mt) REVERT: B 1024 PHE cc_start: 0.9015 (m-80) cc_final: 0.8672 (m-80) REVERT: B 1067 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9232 (tp) REVERT: B 1075 ILE cc_start: 0.8753 (mt) cc_final: 0.8493 (mt) REVERT: C 610 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8642 (mmtp) REVERT: C 852 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7418 (mmm-85) REVERT: C 981 GLU cc_start: 0.8047 (tp30) cc_final: 0.7834 (tp30) REVERT: C 985 SER cc_start: 0.9249 (t) cc_final: 0.8817 (p) REVERT: C 1075 ILE cc_start: 0.8810 (mt) cc_final: 0.8455 (mm) outliers start: 64 outliers final: 26 residues processed: 353 average time/residue: 0.2784 time to fit residues: 158.0827 Evaluate side-chains 295 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 266 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 947 PHE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 933 HIS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN D1000 GLN B 893 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20916 Z= 0.242 Angle : 0.585 8.803 28168 Z= 0.274 Chirality : 0.042 0.174 3224 Planarity : 0.004 0.059 3392 Dihedral : 19.816 152.312 3600 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.07 % Allowed : 13.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2436 helix: 0.88 (0.13), residues: 1740 sheet: 4.34 (0.88), residues: 48 loop : -0.51 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 515 HIS 0.006 0.001 HIS B 494 PHE 0.011 0.001 PHE C1022 TYR 0.012 0.001 TYR D 840 ARG 0.003 0.000 ARG D 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 272 time to evaluate : 2.291 Fit side-chains REVERT: A 681 GLU cc_start: 0.7869 (pm20) cc_final: 0.7655 (pm20) REVERT: A 721 MET cc_start: 0.7788 (tpp) cc_final: 0.7550 (mmp) REVERT: A 785 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: A 852 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7480 (mmm-85) REVERT: A 941 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9078 (tp) REVERT: D 852 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7229 (mmm-85) REVERT: D 981 GLU cc_start: 0.8148 (tp30) cc_final: 0.7932 (tp30) REVERT: D 985 SER cc_start: 0.9379 (t) cc_final: 0.8903 (p) REVERT: D 996 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8309 (mmm-85) REVERT: B 785 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: B 852 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: B 891 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9049 (mp) REVERT: B 911 MET cc_start: 0.8711 (mtp) cc_final: 0.8329 (mtm) REVERT: B 941 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8948 (tp) REVERT: B 987 GLU cc_start: 0.8415 (tt0) cc_final: 0.8192 (tt0) REVERT: B 1024 PHE cc_start: 0.8974 (m-80) cc_final: 0.8735 (m-80) REVERT: B 1075 ILE cc_start: 0.8897 (mt) cc_final: 0.8668 (mp) REVERT: C 610 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8711 (mmtp) REVERT: C 852 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: C 981 GLU cc_start: 0.8058 (tp30) cc_final: 0.7857 (tp30) REVERT: C 985 SER cc_start: 0.9346 (t) cc_final: 0.8924 (p) REVERT: C 998 VAL cc_start: 0.9169 (p) cc_final: 0.8760 (m) outliers start: 64 outliers final: 34 residues processed: 316 average time/residue: 0.2913 time to fit residues: 145.5523 Evaluate side-chains 281 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1002 SER Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0870 chunk 133 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 chunk 175 optimal weight: 0.0770 chunk 97 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 211 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN A 619 ASN D 619 ASN D 687 ASN B 687 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 687 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20916 Z= 0.131 Angle : 0.537 9.292 28168 Z= 0.251 Chirality : 0.039 0.182 3224 Planarity : 0.003 0.051 3392 Dihedral : 18.771 158.840 3600 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 15.69 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2436 helix: 1.21 (0.13), residues: 1736 sheet: 4.18 (0.85), residues: 48 loop : -0.25 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.003 0.001 HIS C 481 PHE 0.009 0.001 PHE D 823 TYR 0.017 0.001 TYR C 768 ARG 0.003 0.000 ARG D 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 2.353 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7706 (tpp) cc_final: 0.7491 (mmp) REVERT: A 785 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (m-10) REVERT: A 852 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7513 (mmm-85) REVERT: D 504 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8509 (mmmm) REVERT: D 852 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7228 (mmm-85) REVERT: D 985 SER cc_start: 0.9309 (t) cc_final: 0.8966 (p) REVERT: D 987 GLU cc_start: 0.8354 (tt0) cc_final: 0.7965 (tt0) REVERT: B 785 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: B 852 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7285 (mmm-85) REVERT: B 941 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 1024 PHE cc_start: 0.8986 (m-80) cc_final: 0.8681 (m-80) REVERT: C 610 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8680 (mmtp) REVERT: C 852 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7431 (mmm-85) REVERT: C 985 SER cc_start: 0.9299 (t) cc_final: 0.8898 (p) outliers start: 40 outliers final: 21 residues processed: 299 average time/residue: 0.3077 time to fit residues: 143.9107 Evaluate side-chains 271 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 0.2980 chunk 195 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 GLN B 907 GLN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20916 Z= 0.233 Angle : 0.573 11.505 28168 Z= 0.269 Chirality : 0.041 0.157 3224 Planarity : 0.003 0.050 3392 Dihedral : 18.146 163.695 3600 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.50 % Allowed : 16.31 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2436 helix: 1.37 (0.13), residues: 1740 sheet: 4.36 (0.83), residues: 48 loop : -0.27 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 515 HIS 0.006 0.001 HIS B 494 PHE 0.018 0.001 PHE C 818 TYR 0.010 0.001 TYR A 840 ARG 0.010 0.000 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 2.269 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7812 (tpp) cc_final: 0.7570 (mmp) REVERT: A 785 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: D 852 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7241 (mmm-85) REVERT: D 987 GLU cc_start: 0.8429 (tt0) cc_final: 0.8080 (tt0) REVERT: B 785 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: B 852 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7274 (mmm-85) REVERT: B 941 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9056 (tp) REVERT: C 530 MET cc_start: 0.8055 (mmm) cc_final: 0.7642 (mtt) REVERT: C 610 LYS cc_start: 0.9059 (mmtp) cc_final: 0.8767 (mmtp) REVERT: C 852 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7451 (mmm-85) REVERT: C 941 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9034 (tp) outliers start: 52 outliers final: 30 residues processed: 285 average time/residue: 0.3011 time to fit residues: 136.0533 Evaluate side-chains 275 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1002 SER Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 131 optimal weight: 0.0470 chunk 235 optimal weight: 0.7980 chunk 147 optimal weight: 0.0570 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20916 Z= 0.135 Angle : 0.531 10.005 28168 Z= 0.248 Chirality : 0.039 0.135 3224 Planarity : 0.003 0.048 3392 Dihedral : 17.599 167.286 3600 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.92 % Allowed : 16.70 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2436 helix: 1.51 (0.13), residues: 1736 sheet: 4.29 (0.82), residues: 48 loop : -0.07 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 515 HIS 0.003 0.000 HIS C 481 PHE 0.009 0.001 PHE B 859 TYR 0.019 0.001 TYR C 768 ARG 0.005 0.000 ARG D 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 721 MET cc_start: 0.7771 (tpp) cc_final: 0.7565 (mmp) REVERT: A 785 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: D 852 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7264 (mmm-85) REVERT: D 985 SER cc_start: 0.9386 (t) cc_final: 0.9099 (p) REVERT: D 987 GLU cc_start: 0.8370 (tt0) cc_final: 0.7987 (tt0) REVERT: B 785 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: B 852 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7265 (mmm-85) REVERT: B 941 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8983 (tp) REVERT: B 1024 PHE cc_start: 0.8975 (m-80) cc_final: 0.8632 (m-80) REVERT: C 464 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7280 (ttp80) REVERT: C 610 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8679 (mmtp) REVERT: C 733 MET cc_start: 0.8336 (tpp) cc_final: 0.7551 (ttp) REVERT: C 852 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: C 912 MET cc_start: 0.8525 (ttp) cc_final: 0.8305 (ttm) REVERT: C 941 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9016 (tp) REVERT: C 985 SER cc_start: 0.9362 (t) cc_final: 0.9093 (p) outliers start: 40 outliers final: 28 residues processed: 284 average time/residue: 0.2937 time to fit residues: 132.7720 Evaluate side-chains 280 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20916 Z= 0.224 Angle : 0.555 10.236 28168 Z= 0.261 Chirality : 0.040 0.152 3224 Planarity : 0.003 0.049 3392 Dihedral : 17.296 174.496 3600 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.87 % Allowed : 17.23 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2436 helix: 1.54 (0.13), residues: 1740 sheet: 4.23 (0.82), residues: 48 loop : -0.16 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 515 HIS 0.006 0.001 HIS B 494 PHE 0.019 0.001 PHE B1022 TYR 0.012 0.001 TYR D 840 ARG 0.005 0.000 ARG D 996 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 245 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7815 (tpp) cc_final: 0.7584 (mmp) REVERT: A 785 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: D 852 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7230 (mmm-85) REVERT: D 987 GLU cc_start: 0.8425 (tt0) cc_final: 0.8076 (tt0) REVERT: B 530 MET cc_start: 0.8462 (mmm) cc_final: 0.8049 (mtt) REVERT: B 785 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7748 (m-10) REVERT: B 852 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: C 464 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7325 (ttp80) REVERT: C 610 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8771 (mmtp) REVERT: C 852 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7425 (mmm-85) REVERT: C 912 MET cc_start: 0.8648 (ttp) cc_final: 0.8400 (ttm) outliers start: 39 outliers final: 31 residues processed: 270 average time/residue: 0.2894 time to fit residues: 125.2263 Evaluate side-chains 268 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 218 optimal weight: 0.0370 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20916 Z= 0.164 Angle : 0.529 9.321 28168 Z= 0.250 Chirality : 0.039 0.136 3224 Planarity : 0.003 0.049 3392 Dihedral : 16.938 179.636 3600 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.06 % Allowed : 16.94 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2436 helix: 1.57 (0.13), residues: 1740 sheet: 4.18 (0.81), residues: 48 loop : -0.09 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 809 HIS 0.003 0.001 HIS D 494 PHE 0.014 0.001 PHE B 859 TYR 0.019 0.001 TYR C 768 ARG 0.007 0.000 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7788 (tpp) cc_final: 0.7569 (mmp) REVERT: A 785 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: D 852 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7154 (mmm-85) REVERT: D 987 GLU cc_start: 0.8398 (tt0) cc_final: 0.8038 (tt0) REVERT: B 530 MET cc_start: 0.8659 (mmm) cc_final: 0.8053 (mtt) REVERT: B 785 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7709 (m-10) REVERT: B 852 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7255 (mmm-85) REVERT: C 464 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7333 (ttp80) REVERT: C 610 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8782 (mmtp) REVERT: C 842 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8499 (m-80) REVERT: C 852 ARG cc_start: 0.7769 (mmm-85) cc_final: 0.7387 (mmm-85) REVERT: C 912 MET cc_start: 0.8576 (ttp) cc_final: 0.8331 (ttm) outliers start: 43 outliers final: 33 residues processed: 275 average time/residue: 0.2880 time to fit residues: 125.9232 Evaluate side-chains 273 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 118 optimal weight: 0.0000 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20916 Z= 0.151 Angle : 0.532 9.995 28168 Z= 0.250 Chirality : 0.039 0.131 3224 Planarity : 0.003 0.050 3392 Dihedral : 16.544 176.988 3600 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 17.51 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.18), residues: 2436 helix: 1.65 (0.13), residues: 1740 sheet: 4.21 (0.81), residues: 48 loop : -0.08 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 515 HIS 0.003 0.000 HIS B 494 PHE 0.018 0.001 PHE A1022 TYR 0.017 0.001 TYR B 768 ARG 0.011 0.000 ARG C 996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 251 time to evaluate : 2.290 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7779 (tpp) cc_final: 0.7561 (mmp) REVERT: A 785 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (m-10) REVERT: D 852 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: D 985 SER cc_start: 0.9386 (t) cc_final: 0.9145 (p) REVERT: D 987 GLU cc_start: 0.8393 (tt0) cc_final: 0.8050 (tt0) REVERT: B 530 MET cc_start: 0.8709 (mmm) cc_final: 0.8489 (mtp) REVERT: B 785 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: B 852 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.7254 (mmm-85) REVERT: C 464 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7356 (ttp80) REVERT: C 530 MET cc_start: 0.8360 (mmm) cc_final: 0.7875 (mtt) REVERT: C 610 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8810 (mmtp) REVERT: C 842 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: C 852 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7377 (mmm-85) REVERT: C 912 MET cc_start: 0.8597 (ttp) cc_final: 0.8321 (ttm) outliers start: 37 outliers final: 29 residues processed: 275 average time/residue: 0.2927 time to fit residues: 128.4371 Evaluate side-chains 269 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 935 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1045 LEU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 935 VAL Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1073 GLU Chi-restraints excluded: chain C residue 1075 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 178 optimal weight: 0.0370 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085191 restraints weight = 32742.104| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.71 r_work: 0.2876 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20916 Z= 0.147 Angle : 0.530 8.891 28168 Z= 0.251 Chirality : 0.039 0.151 3224 Planarity : 0.003 0.048 3392 Dihedral : 16.264 179.676 3600 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.82 % Allowed : 17.32 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2436 helix: 1.74 (0.13), residues: 1716 sheet: 4.16 (0.81), residues: 48 loop : -0.22 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 809 HIS 0.003 0.000 HIS C 481 PHE 0.015 0.001 PHE C 859 TYR 0.020 0.001 TYR C 768 ARG 0.010 0.000 ARG C 996 =============================================================================== Job complete usr+sys time: 4108.10 seconds wall clock time: 77 minutes 2.61 seconds (4622.61 seconds total)