Starting phenix.real_space_refine on Tue Dec 12 05:41:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqo_20449/12_2023/6pqo_20449_updated.pdb" } resolution = 2.88 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= 0.008 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 144 5.16 5 C 13360 2.51 5 N 3208 2.21 5 O 3576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 592": "NH1" <-> "NH2" Residue "D ARG 604": "NH1" <-> "NH2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D ARG 975": "NH1" <-> "NH2" Residue "D ARG 996": "NH1" <-> "NH2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 996": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 604": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 852": "NH1" <-> "NH2" 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 ARG 717": "NH1" <-> "NH2" Residue "C ARG 852": "NH1" <-> "NH2" 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4813 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 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: "D" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 278 Unusual residues: {'6OU': 5, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'6OU': 3, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 82 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 237 Unusual residues: {'6OU': 4, 'JT0': 1, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'6OU:plan-1': 3, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 11.34, per 1000 atoms: 0.56 Number of scatterers: 20312 At special positions: 0 Unit cell: (113.4, 113.4, 149.04, 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 144 16.00 P 24 15.00 O 3576 8.00 N 3208 7.00 C 13360 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 D 747 " " NAG F 1 " - " ASN A 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: 8.37 Conformation dependent library (CDL) restraints added in 3.5 seconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... 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 492 removed outlier: 3.674A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) 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: 3.690A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' 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: 3.797A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR D 772 " --> pdb=" O TYR D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 817 Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 850 " --> pdb=" O PHE D 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 891 removed outlier: 5.286A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 4.801A 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 926 No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.782A 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 1016 through 1023 Processing helix chain 'D' and resid 1040 through 1071 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 492 removed outlier: 3.675A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) 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: 3.690A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 684 through 690 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: 3.796A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 795 removed outlier: 3.697A pdb=" N THR A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 817 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.707A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 850 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 5.287A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 4.801A 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 926 No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 986 removed outlier: 4.169A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.782A 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 1016 through 1023 Processing helix chain 'A' 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 492 removed outlier: 3.675A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) 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: 3.690A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' 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: 3.797A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR B 772 " --> pdb=" O TYR B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 817 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 850 " --> pdb=" O PHE B 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 891 removed outlier: 5.287A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 4.800A 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 926 No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.782A 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 1016 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 492 removed outlier: 3.675A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) 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: 3.691A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 669 No H-bonds generated for 'chain 'C' and resid 667 through 669' 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: 3.797A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 795 removed outlier: 3.698A pdb=" N THR C 772 " --> pdb=" O TYR C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 817 Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.706A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 850 " --> pdb=" O PHE C 846 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 5.285A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 4.800A 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 926 No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 986 removed outlier: 4.168A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.782A 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 1016 through 1023 Processing helix chain 'C' and resid 1040 through 1071 Processing sheet with id= A, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.001A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= F, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= H, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.002A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2913 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: 6.20 Time building geometry restraints manager: 8.64 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: 3060 1.30 - 1.43: 5286 1.43 - 1.56: 11863 1.56 - 1.69: 235 1.69 - 1.81: 276 Bond restraints: 20720 Sorted by residual: bond pdb=" C09 JT0 B1204 " pdb=" S21 JT0 B1204 " ideal model delta sigma weight residual 1.543 1.773 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C09 JT0 D1303 " pdb=" S21 JT0 D1303 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C09 JT0 A1204 " pdb=" S21 JT0 A1204 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C09 JT0 C1205 " pdb=" S21 JT0 C1205 " ideal model delta sigma weight residual 1.543 1.772 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C20 JT0 C1205 " pdb=" S21 JT0 C1205 " ideal model delta sigma weight residual 1.515 1.725 -0.210 2.00e-02 2.50e+03 1.11e+02 ... (remaining 20715 not shown) Histogram of bond angle deviations from ideal: 89.06 - 98.06: 8 98.06 - 107.06: 700 107.06 - 116.05: 12957 116.05 - 125.05: 13890 125.05 - 134.05: 389 Bond angle restraints: 27944 Sorted by residual: angle pdb=" C18 JT0 B1204 " pdb=" C15 JT0 B1204 " pdb=" O16 JT0 B1204 " ideal model delta sigma weight residual 87.26 120.92 -33.66 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 D1303 " pdb=" C15 JT0 D1303 " pdb=" O16 JT0 D1303 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 C1205 " pdb=" C15 JT0 C1205 " pdb=" O16 JT0 C1205 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C18 JT0 A1204 " pdb=" C15 JT0 A1204 " pdb=" O16 JT0 A1204 " ideal model delta sigma weight residual 87.26 120.89 -33.63 3.00e+00 1.11e-01 1.26e+02 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 107.73 123.67 -15.94 1.56e+00 4.11e-01 1.04e+02 ... (remaining 27939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 12260 35.43 - 70.86: 328 70.86 - 106.29: 60 106.29 - 141.72: 20 141.72 - 177.15: 12 Dihedral angle restraints: 12680 sinusoidal: 5460 harmonic: 7220 Sorted by residual: 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 98.25 177.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN C1207 " pdb=" O1 LBN C1207 " pdb=" P1 LBN C1207 " pdb=" O3 LBN C1207 " ideal model delta sinusoidal sigma weight residual 275.40 98.27 177.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D1305 " pdb=" O1 LBN D1305 " pdb=" P1 LBN D1305 " pdb=" O3 LBN D1305 " ideal model delta sinusoidal sigma weight residual 275.40 98.28 177.12 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 3180 0.182 - 0.364: 8 0.364 - 0.546: 8 0.546 - 0.728: 12 0.728 - 0.910: 4 Chirality restraints: 3212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.23e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.16e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.15e+01 ... (remaining 3209 not shown) Planarity restraints: 3368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 JT0 C1205 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 C1205 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 C1205 " 0.471 2.00e-02 2.50e+03 pdb=" C22 JT0 C1205 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 C1205 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 C1205 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 D1303 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 D1303 " -0.641 2.00e-02 2.50e+03 pdb=" C09 JT0 D1303 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 D1303 " -1.000 2.00e-02 2.50e+03 pdb=" N03 JT0 D1303 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 D1303 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 JT0 B1204 " 0.148 2.00e-02 2.50e+03 6.51e-01 6.36e+03 pdb=" C04 JT0 B1204 " -0.642 2.00e-02 2.50e+03 pdb=" C09 JT0 B1204 " 0.472 2.00e-02 2.50e+03 pdb=" C22 JT0 B1204 " -0.999 2.00e-02 2.50e+03 pdb=" N03 JT0 B1204 " 0.081 2.00e-02 2.50e+03 pdb=" O01 JT0 B1204 " 0.939 2.00e-02 2.50e+03 ... (remaining 3365 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3044 2.76 - 3.29: 18295 3.29 - 3.83: 31504 3.83 - 4.36: 36793 4.36 - 4.90: 63035 Nonbonded interactions: 152671 Sorted by model distance: nonbonded pdb=" OD1 ASN B 747 " pdb=" N SER B 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN D 747 " pdb=" N SER D 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN A 747 " pdb=" N SER A 748 " model vdw 2.222 2.520 nonbonded pdb=" OD1 ASN C 747 " pdb=" N SER C 748 " model vdw 2.223 2.520 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.301 2.440 ... (remaining 152666 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 1208 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 1208)) selection = (chain 'C' and (resid 446 through 1079 or (resid 1208 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 'D' and (resid 446 through 1079 or (resid 1308 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.910 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 54.210 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 0.230 20720 Z= 0.786 Angle : 1.413 33.663 27944 Z= 0.606 Chirality : 0.079 0.910 3212 Planarity : 0.026 0.651 3364 Dihedral : 18.187 177.148 7984 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % 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: -2.93 (0.14), residues: 2416 helix: -2.04 (0.10), residues: 1732 sheet: 0.83 (0.76), residues: 68 loop : -1.27 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 515 HIS 0.011 0.002 HIS A 585 PHE 0.027 0.003 PHE C 783 TYR 0.034 0.003 TYR B 785 ARG 0.015 0.001 ARG C 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 602 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 610 average time/residue: 1.3501 time to fit residues: 926.1733 Evaluate side-chains 281 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 278 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 3.4872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 451 HIS D 512 HIS D 519 HIS D 549 ASN D 644 HIS D 700 HIS D 719 HIS D 805 ASN D 970 HIS D 983 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 460 ASN A 512 HIS A 519 HIS A 549 ASN A 644 HIS A 700 HIS A 719 HIS A 851 GLN A 970 HIS A 983 HIS B 451 HIS B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 719 HIS B 805 ASN B 851 GLN B 917 ASN B 970 HIS B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 512 HIS C 519 HIS C 570 HIS C 577 ASN C 644 HIS C 700 HIS C 739 ASN C 970 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20720 Z= 0.187 Angle : 0.633 10.230 27944 Z= 0.299 Chirality : 0.041 0.156 3212 Planarity : 0.005 0.056 3364 Dihedral : 19.196 157.613 3512 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.18 % Allowed : 14.69 % Favored : 81.13 % 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: -0.76 (0.16), residues: 2416 helix: -0.29 (0.12), residues: 1724 sheet: 2.34 (0.86), residues: 48 loop : -0.94 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 515 HIS 0.007 0.001 HIS B 970 PHE 0.013 0.001 PHE C 823 TYR 0.015 0.001 TYR A 785 ARG 0.006 0.001 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 306 time to evaluate : 2.696 Fit side-chains outliers start: 86 outliers final: 25 residues processed: 372 average time/residue: 1.2047 time to fit residues: 512.5026 Evaluate side-chains 271 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 10 average time/residue: 0.7131 time to fit residues: 12.0206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 0.0060 chunk 61 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 40.0000 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 40.0000 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 HIS D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN A 805 ASN B 560 HIS B 855 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 577 ASN C 805 ASN C 970 HIS C 983 HIS C1000 GLN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20720 Z= 0.198 Angle : 0.564 7.884 27944 Z= 0.275 Chirality : 0.040 0.180 3212 Planarity : 0.004 0.059 3364 Dihedral : 17.622 162.346 3512 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.72 % Allowed : 15.61 % Favored : 79.67 % 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: 2416 helix: 0.51 (0.12), residues: 1732 sheet: 2.73 (0.86), residues: 48 loop : -0.68 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 515 HIS 0.005 0.001 HIS D 585 PHE 0.011 0.001 PHE A 818 TYR 0.017 0.001 TYR A 785 ARG 0.005 0.001 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 264 time to evaluate : 2.567 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 40 residues processed: 336 average time/residue: 1.2040 time to fit residues: 462.9530 Evaluate side-chains 279 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 239 time to evaluate : 2.309 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 28 residues processed: 12 average time/residue: 0.4150 time to fit residues: 10.0352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 0.0020 chunk 116 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 460 ASN D 687 ASN D 691 GLN D 907 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A 907 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 687 ASN B 691 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS C 917 ASN ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20720 Z= 0.134 Angle : 0.504 8.282 27944 Z= 0.249 Chirality : 0.038 0.161 3212 Planarity : 0.004 0.053 3364 Dihedral : 16.892 167.860 3512 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.84 % Allowed : 16.97 % Favored : 79.18 % 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: 0.97 (0.17), residues: 2416 helix: 1.09 (0.13), residues: 1720 sheet: 2.89 (0.86), residues: 48 loop : -0.58 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS D 970 PHE 0.011 0.001 PHE D 669 TYR 0.011 0.001 TYR A 785 ARG 0.004 0.000 ARG C 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 264 time to evaluate : 2.579 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 36 residues processed: 317 average time/residue: 1.2601 time to fit residues: 458.2418 Evaluate side-chains 271 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 2.371 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 27 residues processed: 9 average time/residue: 0.4707 time to fit residues: 8.7335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN B 907 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20720 Z= 0.180 Angle : 0.514 8.042 27944 Z= 0.255 Chirality : 0.039 0.150 3212 Planarity : 0.004 0.054 3364 Dihedral : 16.204 171.055 3512 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.09 % Allowed : 17.70 % Favored : 78.21 % 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: 1.23 (0.17), residues: 2416 helix: 1.28 (0.13), residues: 1736 sheet: 2.98 (0.84), residues: 48 loop : -0.53 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 515 HIS 0.004 0.001 HIS D 585 PHE 0.010 0.001 PHE D 818 TYR 0.012 0.001 TYR A 785 ARG 0.004 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 245 time to evaluate : 2.213 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 44 residues processed: 296 average time/residue: 1.2514 time to fit residues: 422.0075 Evaluate side-chains 281 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 28 residues processed: 16 average time/residue: 0.6060 time to fit residues: 15.6800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 691 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS C 907 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: 0.7032 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20720 Z= 0.238 Angle : 0.539 8.412 27944 Z= 0.268 Chirality : 0.040 0.155 3212 Planarity : 0.004 0.054 3364 Dihedral : 15.828 171.497 3512 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.18 % Allowed : 18.24 % Favored : 77.58 % 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: 1.23 (0.17), residues: 2416 helix: 1.29 (0.13), residues: 1736 sheet: 3.06 (0.83), residues: 48 loop : -0.57 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 515 HIS 0.005 0.001 HIS D 585 PHE 0.011 0.001 PHE A 818 TYR 0.013 0.001 TYR A 785 ARG 0.004 0.001 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 234 time to evaluate : 2.478 Fit side-chains outliers start: 86 outliers final: 41 residues processed: 290 average time/residue: 1.2680 time to fit residues: 420.3993 Evaluate side-chains 269 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 28 residues processed: 13 average time/residue: 0.6837 time to fit residues: 14.3060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20720 Z= 0.170 Angle : 0.499 7.575 27944 Z= 0.249 Chirality : 0.039 0.150 3212 Planarity : 0.004 0.051 3364 Dihedral : 15.425 174.337 3512 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.97 % Allowed : 19.41 % Favored : 77.63 % 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: 1.40 (0.18), residues: 2416 helix: 1.45 (0.13), residues: 1736 sheet: 3.13 (0.82), residues: 48 loop : -0.61 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 515 HIS 0.004 0.001 HIS D 585 PHE 0.008 0.001 PHE B 583 TYR 0.009 0.001 TYR A 785 ARG 0.005 0.001 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 239 time to evaluate : 2.521 Fit side-chains outliers start: 61 outliers final: 40 residues processed: 278 average time/residue: 1.2923 time to fit residues: 409.6593 Evaluate side-chains 267 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 32 residues processed: 8 average time/residue: 0.6966 time to fit residues: 9.8521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 570 HIS A 687 ASN B1047 GLN C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20720 Z= 0.277 Angle : 0.572 8.528 27944 Z= 0.284 Chirality : 0.042 0.209 3212 Planarity : 0.004 0.051 3364 Dihedral : 15.326 171.608 3512 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.21 % Allowed : 19.60 % Favored : 77.19 % 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: 1.29 (0.17), residues: 2416 helix: 1.32 (0.13), residues: 1732 sheet: 3.14 (0.82), residues: 48 loop : -0.50 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 515 HIS 0.006 0.001 HIS D 585 PHE 0.012 0.002 PHE D 583 TYR 0.011 0.001 TYR A 785 ARG 0.007 0.001 ARG D 717 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 2.374 Fit side-chains outliers start: 66 outliers final: 41 residues processed: 286 average time/residue: 1.3111 time to fit residues: 425.9867 Evaluate side-chains 269 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 8 average time/residue: 0.3390 time to fit residues: 6.9870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.0040 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20720 Z= 0.145 Angle : 0.502 8.213 27944 Z= 0.252 Chirality : 0.039 0.162 3212 Planarity : 0.004 0.051 3364 Dihedral : 15.051 176.281 3512 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.09 % Allowed : 20.87 % Favored : 77.04 % 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: 1.51 (0.18), residues: 2416 helix: 1.53 (0.13), residues: 1736 sheet: 3.24 (0.81), residues: 48 loop : -0.58 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 832 HIS 0.003 0.001 HIS D 585 PHE 0.009 0.001 PHE C 583 TYR 0.008 0.001 TYR D1049 ARG 0.006 0.001 ARG D 717 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 241 time to evaluate : 2.155 Fit side-chains outliers start: 43 outliers final: 32 residues processed: 277 average time/residue: 1.0468 time to fit residues: 330.6063 Evaluate side-chains 263 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.4179 time to fit residues: 5.6178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 193 optimal weight: 0.9990 chunk 20 optimal weight: 0.0040 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20720 Z= 0.151 Angle : 0.509 9.010 27944 Z= 0.254 Chirality : 0.038 0.135 3212 Planarity : 0.004 0.050 3364 Dihedral : 14.880 178.025 3512 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.75 % Allowed : 21.11 % Favored : 77.14 % 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: 1.61 (0.18), residues: 2416 helix: 1.59 (0.13), residues: 1736 sheet: 3.35 (0.81), residues: 48 loop : -0.52 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 809 HIS 0.003 0.001 HIS D 585 PHE 0.012 0.001 PHE C 669 TYR 0.007 0.001 TYR A 785 ARG 0.007 0.001 ARG A 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 2.581 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 267 average time/residue: 1.2703 time to fit residues: 387.0292 Evaluate side-chains 256 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 3.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 463 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS ** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.095781 restraints weight = 24947.476| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.15 r_work: 0.2885 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20720 Z= 0.210 Angle : 0.530 9.744 27944 Z= 0.263 Chirality : 0.040 0.142 3212 Planarity : 0.004 0.052 3364 Dihedral : 14.879 177.162 3512 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 20.87 % Favored : 76.95 % 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: 1.52 (0.18), residues: 2416 helix: 1.52 (0.13), residues: 1732 sheet: 3.34 (0.81), residues: 48 loop : -0.50 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 515 HIS 0.005 0.001 HIS D 585 PHE 0.010 0.001 PHE A 583 TYR 0.010 0.001 TYR D1049 ARG 0.007 0.001 ARG A 717 =============================================================================== Job complete usr+sys time: 7721.00 seconds wall clock time: 138 minutes 9.31 seconds (8289.31 seconds total)