Starting phenix.real_space_refine on Thu Aug 8 00:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/08_2024/6pqp_20450.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/08_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_20450/08_2024/6pqp_20450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/08_2024/6pqp_20450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/08_2024/6pqp_20450.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqp_20450/08_2024/6pqp_20450.cif" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 10.98, per 1000 atoms: 0.54 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: 7.44 Conformation dependent library (CDL) restraints added in 3.3 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... Secondary structure from input PDB file: 144 helices and 8 sheets defined 73.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.513A pdb=" N TYR A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR A 670 " --> pdb=" O PRO A 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 671' Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 739 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 766 through 796 removed outlier: 3.586A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 846 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) Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN A 851 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER A 899 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1016 through 1024 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.512A pdb=" N TYR D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 537 Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 671 removed outlier: 3.766A pdb=" N THR D 670 " --> pdb=" O PRO D 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 666 through 671' Processing helix chain 'D' and resid 672 through 677 Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 removed outlier: 3.584A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 739 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 766 through 796 removed outlier: 3.586A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.760A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 846 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) Processing helix chain 'D' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN D 851 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER D 899 " --> pdb=" O ASP D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1016 through 1024 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.524A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.612A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.853A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 671' Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 739 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 766 through 796 removed outlier: 3.586A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 846 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) Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN B 851 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE B 877 " --> pdb=" O SER B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.614A pdb=" N SER B 899 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.987A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1016 through 1024 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.513A pdb=" N TYR C 456 " --> pdb=" O PHE C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.525A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 537 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.520A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.613A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.852A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 640 removed outlier: 4.058A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 671 removed outlier: 3.765A pdb=" N THR C 670 " --> pdb=" O PRO C 666 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 671 " --> pdb=" O LEU C 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 666 through 671' Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 removed outlier: 3.583A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 739 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 766 through 796 removed outlier: 3.587A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.759A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 846 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) Processing helix chain 'C' and resid 847 through 851 removed outlier: 3.683A pdb=" N GLN C 851 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 873 removed outlier: 3.684A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 892 removed outlier: 3.650A pdb=" N PHE C 877 " --> pdb=" O SER C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 3.613A pdb=" N SER C 899 " --> pdb=" O ASP C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 970 removed outlier: 4.076A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.988A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1016 through 1024 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 656 through 659 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 656 through 659 Processing sheet with id=AA4, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 656 through 659 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.157A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3471 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: 6.25 Time building geometry restraints manager: 7.90 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: 347 2.69 - 3.24: 18481 3.24 - 3.79: 30503 3.79 - 4.35: 40445 4.35 - 4.90: 66550 Nonbonded interactions: 156326 Sorted by model distance: nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.132 3.120 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.132 3.120 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.284 3.040 ... (remaining 156321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.810 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.100 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.970 ------------------------------------------------------------------------------- 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= 0.771 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 : 2.188 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: 0.3190 time to fit residues: 296.1390 Evaluate side-chains 308 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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: 3.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 HIS ** D 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 577 ASN B 590 ASN 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 512 HIS C 519 HIS ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 590 ASN C 644 HIS ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20916 Z= 0.189 Angle : 0.672 10.120 28168 Z= 0.317 Chirality : 0.045 0.272 3224 Planarity : 0.005 0.066 3392 Dihedral : 23.038 156.469 3606 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.30 % Allowed : 11.71 % Favored : 85.99 % 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: -0.78 (0.16), residues: 2436 helix: -0.31 (0.11), residues: 1760 sheet: 1.63 (0.79), residues: 68 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 515 HIS 0.004 0.001 HIS A 970 PHE 0.014 0.001 PHE D 823 TYR 0.015 0.001 TYR D 768 ARG 0.006 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 411 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 363 time to evaluate : 2.347 Fit side-chains revert: symmetry clash REVERT: A 625 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8435 (mm-30) REVERT: A 721 MET cc_start: 0.7886 (tpp) cc_final: 0.7646 (mmp) REVERT: A 783 PHE cc_start: 0.8038 (m-10) cc_final: 0.7754 (m-10) REVERT: A 1042 MET cc_start: 0.7520 (ppp) cc_final: 0.7235 (ptt) REVERT: D 504 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8525 (mmmm) REVERT: D 610 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8787 (mmtp) REVERT: D 768 TYR cc_start: 0.7367 (p90) cc_final: 0.7153 (p90) REVERT: D 981 GLU cc_start: 0.8081 (tp30) cc_final: 0.7705 (tp30) REVERT: D 985 SER cc_start: 0.9320 (t) cc_final: 0.8574 (p) REVERT: B 985 SER cc_start: 0.9265 (t) cc_final: 0.8997 (p) REVERT: B 1024 PHE cc_start: 0.9116 (m-80) cc_final: 0.8730 (m-80) REVERT: B 1073 GLU cc_start: 0.7259 (tt0) cc_final: 0.6901 (tt0) REVERT: B 1075 ILE cc_start: 0.8280 (mt) cc_final: 0.7980 (mp) REVERT: C 852 ARG cc_start: 0.7683 (mmm-85) cc_final: 0.7248 (mmm-85) REVERT: C 981 GLU cc_start: 0.8019 (tp30) cc_final: 0.7634 (tp30) REVERT: C 985 SER cc_start: 0.9187 (t) cc_final: 0.8558 (p) REVERT: C 998 VAL cc_start: 0.9119 (p) cc_final: 0.8770 (m) REVERT: C 1075 ILE cc_start: 0.8555 (mt) cc_final: 0.8221 (mp) outliers start: 48 outliers final: 14 residues processed: 394 average time/residue: 0.2807 time to fit residues: 177.2935 Evaluate side-chains 312 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 D residue 510 SER Chi-restraints excluded: chain D residue 775 ILE Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 824 VAL 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 1073 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 221 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 0.0970 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN D 560 HIS D 590 ASN ** D 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 GLN B 893 ASN B1047 GLN C 537 ASN C 687 ASN ** C 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1047 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20916 Z= 0.289 Angle : 0.656 10.666 28168 Z= 0.314 Chirality : 0.044 0.216 3224 Planarity : 0.004 0.063 3392 Dihedral : 21.090 146.806 3600 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.07 % Allowed : 12.43 % Favored : 84.50 % 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: 0.38 (0.17), residues: 2436 helix: 0.60 (0.12), residues: 1752 sheet: 1.86 (0.80), residues: 68 loop : -0.67 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 515 HIS 0.008 0.001 HIS C 494 PHE 0.014 0.002 PHE B 846 TYR 0.021 0.002 TYR C 768 ARG 0.008 0.000 ARG B 996 *********************** 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 382 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 318 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.7867 (tpp) cc_final: 0.7651 (mmp) REVERT: A 783 PHE cc_start: 0.8299 (m-10) cc_final: 0.8022 (m-10) REVERT: A 785 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: A 852 ARG cc_start: 0.7787 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: D 643 LEU cc_start: 0.8235 (mp) cc_final: 0.7887 (mt) REVERT: D 852 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7265 (mmm-85) REVERT: D 981 GLU cc_start: 0.8175 (tp30) cc_final: 0.7961 (tp30) REVERT: D 985 SER cc_start: 0.9332 (t) cc_final: 0.8818 (p) REVERT: D 986 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9165 (tt) REVERT: B 709 MET cc_start: 0.9029 (tmm) cc_final: 0.8761 (tmm) REVERT: B 785 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7382 (m-10) REVERT: B 852 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.7358 (mmm-85) REVERT: B 998 VAL cc_start: 0.9177 (p) cc_final: 0.8684 (m) REVERT: B 1024 PHE cc_start: 0.9165 (m-80) cc_final: 0.8867 (m-80) REVERT: B 1047 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: B 1059 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7848 (mm-30) REVERT: C 610 LYS cc_start: 0.9017 (mmtp) cc_final: 0.8667 (mmtp) REVERT: C 709 MET cc_start: 0.9036 (tmm) cc_final: 0.8817 (tmm) REVERT: C 852 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: C 981 GLU cc_start: 0.8113 (tp30) cc_final: 0.7903 (tp30) REVERT: C 985 SER cc_start: 0.9314 (t) cc_final: 0.8782 (p) REVERT: C 998 VAL cc_start: 0.9256 (p) cc_final: 0.8864 (m) REVERT: C 1075 ILE cc_start: 0.8854 (mt) cc_final: 0.8559 (mm) outliers start: 64 outliers final: 26 residues processed: 364 average time/residue: 0.3036 time to fit residues: 174.4905 Evaluate side-chains 289 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 536 THR Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 785 TYR 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 709 MET Chi-restraints excluded: chain D residue 779 LEU 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 D residue 986 LEU Chi-restraints excluded: chain D residue 1002 SER Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 887 SER 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 B residue 1047 GLN Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 887 SER Chi-restraints excluded: chain C residue 904 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: 0.8980 chunk 115 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: