Starting phenix.real_space_refine on Sat Mar 16 03:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jmn_22397/03_2024/7jmn_22397.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 8610 2.51 5 N 2391 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 85": "NH1" <-> "NH2" Residue "E PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E GLU 641": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "E ARG 755": "NH1" <-> "NH2" Residue "E GLU 789": "OE1" <-> "OE2" Residue "E ASP 885": "OD1" <-> "OD2" Residue "N PHE 835": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 850": "NH1" <-> "NH2" Residue "N ARG 852": "NH1" <-> "NH2" Residue "N ARG 880": "NH1" <-> "NH2" Residue "N GLU 911": "OE1" <-> "OE2" Residue "N GLU 919": "OE1" <-> "OE2" Residue "N ARG 938": "NH1" <-> "NH2" Residue "N ARG 946": "NH1" <-> "NH2" Residue "N GLU 956": "OE1" <-> "OE2" Residue "N ARG 967": "NH1" <-> "NH2" Residue "P ARG 72": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P GLU 113": "OE1" <-> "OE2" Residue "P ASP 178": "OD1" <-> "OD2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P GLU 283": "OE1" <-> "OE2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 421": "NH1" <-> "NH2" Residue "P ARG 492": "NH1" <-> "NH2" Residue "P GLU 503": "OE1" <-> "OE2" Residue "P GLU 522": "OE1" <-> "OE2" Residue "P TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 859": "NH1" <-> "NH2" Residue "P ARG 920": "NH1" <-> "NH2" Residue "P GLU 944": "OE1" <-> "OE2" Residue "O GLU 278": "OE1" <-> "OE2" Residue "O PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4467 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 34, 'TRANS': 549} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "N" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1439 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "P" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6178 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 49, 'TRANS': 760} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1290 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "X" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 259 Classifications: {'peptide': 52} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 51} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 7.22, per 1000 atoms: 0.53 Number of scatterers: 13633 At special positions: 0 Unit cell: (162.208, 164.4, 104.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2570 8.00 N 2391 7.00 C 8610 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=0, symmetry=0 Time building additional restraints: 5.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 37.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.714A pdb=" N TYR E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 230 removed outlier: 4.364A pdb=" N GLU E 225 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 removed outlier: 4.034A pdb=" N ILE E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS E 242 " --> pdb=" O CYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.880A pdb=" N LEU E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 391 removed outlier: 4.327A pdb=" N ILE E 383 " --> pdb=" O LYS E 379 " (cutoff:3.500A) Proline residue: E 387 - end of helix Processing helix chain 'E' and resid 397 through 405 removed outlier: 4.830A pdb=" N TYR E 402 " --> pdb=" O THR E 399 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.897A pdb=" N CYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.652A pdb=" N GLU E 481 " --> pdb=" O TYR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 515 through 524 removed outlier: 3.864A pdb=" N SER E 524 " --> pdb=" O ARG E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 528 Processing helix chain 'E' and resid 529 through 536 removed outlier: 3.960A pdb=" N LEU E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 535 " --> pdb=" O VAL E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.654A pdb=" N LYS E 540 " --> pdb=" O LYS E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 550 removed outlier: 3.697A pdb=" N GLU E 547 " --> pdb=" O HIS E 543 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU E 548 " --> pdb=" O PRO E 544 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU E 549 " --> pdb=" O LEU E 545 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 550 " --> pdb=" O CYS E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 583 removed outlier: 3.814A pdb=" N GLU E 567 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 572 " --> pdb=" O GLU E 568 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU E 576 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR E 583 " --> pdb=" O PHE E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 613 Proline residue: E 611 - end of helix Processing helix chain 'E' and resid 655 through 668 removed outlier: 3.650A pdb=" N ALA E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 681 Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 691 through 699 removed outlier: 3.750A pdb=" N ALA E 695 " --> pdb=" O ALA E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 718 Processing helix chain 'E' and resid 718 through 723 removed outlier: 3.758A pdb=" N LEU E 722 " --> pdb=" O LEU E 718 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 718 through 723' Processing helix chain 'E' and resid 728 through 757 removed outlier: 4.230A pdb=" N ASN E 740 " --> pdb=" O SER E 736 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL E 742 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS E 744 " --> pdb=" O ASN E 740 " (cutoff:3.500A) Proline residue: E 745 - end of helix removed outlier: 4.070A pdb=" N HIS E 748 " --> pdb=" O LYS E 744 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA E 749 " --> pdb=" O PRO E 745 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 750 " --> pdb=" O LEU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 769 removed outlier: 3.628A pdb=" N LEU E 767 " --> pdb=" O ILE E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 843 through 851 removed outlier: 4.241A pdb=" N GLN E 849 " --> pdb=" O LEU E 845 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 850 " --> pdb=" O ALA E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 867 removed outlier: 3.611A pdb=" N SER E 866 " --> pdb=" O ASP E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 882 Processing helix chain 'N' and resid 800 through 813 removed outlier: 4.156A pdb=" N GLN N 805 " --> pdb=" O ILE N 801 " (cutoff:3.500A) Processing helix chain 'N' and resid 814 through 819 removed outlier: 3.941A pdb=" N ARG N 818 " --> pdb=" O GLU N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 876 through 880 removed outlier: 3.677A pdb=" N ARG N 880 " --> pdb=" O VAL N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 882 through 889 removed outlier: 3.971A pdb=" N ASN N 886 " --> pdb=" O GLU N 882 " (cutoff:3.500A) Processing helix chain 'N' and resid 896 through 914 Proline residue: N 902 - end of helix Processing helix chain 'N' and resid 914 through 920 removed outlier: 3.861A pdb=" N GLN N 918 " --> pdb=" O TRP N 914 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU N 919 " --> pdb=" O GLN N 915 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN N 920 " --> pdb=" O THR N 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 914 through 920' Processing helix chain 'N' and resid 978 through 983 Processing helix chain 'N' and resid 995 through 1012 removed outlier: 4.369A pdb=" N GLY N 999 " --> pdb=" O SER N 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N1006 " --> pdb=" O THR N1002 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N1007 " --> pdb=" O GLY N1003 " (cutoff:3.500A) Proline residue: N1008 - end of helix Processing helix chain 'P' and resid 210 through 213 removed outlier: 4.118A pdb=" N VAL P 213 " --> pdb=" O HIS P 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 210 through 213' Processing helix chain 'P' and resid 563 through 568 removed outlier: 4.096A pdb=" N LYS P 566 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU P 567 " --> pdb=" O GLY P 564 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS P 568 " --> pdb=" O PRO P 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 563 through 568' Processing helix chain 'P' and resid 569 through 575 removed outlier: 3.907A pdb=" N SER P 573 " --> pdb=" O ALA P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 607 through 615 removed outlier: 3.884A pdb=" N THR P 611 " --> pdb=" O LYS P 607 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA P 612 " --> pdb=" O ASP P 608 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 641 Processing helix chain 'P' and resid 654 through 672 removed outlier: 3.920A pdb=" N GLN P 659 " --> pdb=" O ASN P 655 " (cutoff:3.500A) Proline residue: P 660 - end of helix removed outlier: 4.281A pdb=" N LYS P 666 " --> pdb=" O THR P 662 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN P 669 " --> pdb=" O GLY P 665 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU P 670 " --> pdb=" O LYS P 666 " (cutoff:3.500A) Processing helix chain 'P' and resid 699 through 726 removed outlier: 3.642A pdb=" N VAL P 703 " --> pdb=" O ASP P 699 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL P 704 " --> pdb=" O GLU P 700 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP P 705 " --> pdb=" O PRO P 701 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA P 706 " --> pdb=" O GLU P 702 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP P 713 " --> pdb=" O SER P 709 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU P 726 " --> pdb=" O THR P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 742 through 751 removed outlier: 3.970A pdb=" N TYR P 750 " --> pdb=" O ASP P 746 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 790 removed outlier: 3.885A pdb=" N GLY P 769 " --> pdb=" O SER P 765 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 773 " --> pdb=" O GLY P 769 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL P 780 " --> pdb=" O ARG P 776 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL P 781 " --> pdb=" O ARG P 777 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU P 782 " --> pdb=" O LEU P 778 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER P 783 " --> pdb=" O GLN P 779 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG P 787 " --> pdb=" O SER P 783 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA P 788 " --> pdb=" O LEU P 784 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 838 removed outlier: 4.107A pdb=" N ASP P 833 " --> pdb=" O ALA P 829 " (cutoff:3.500A) Processing helix chain 'P' and resid 850 through 868 removed outlier: 4.582A pdb=" N THR P 856 " --> pdb=" O SER P 852 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN P 857 " --> pdb=" O GLY P 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS P 861 " --> pdb=" O GLN P 857 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA P 862 " --> pdb=" O ILE P 858 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER P 863 " --> pdb=" O ARG P 859 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY P 866 " --> pdb=" O ALA P 862 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN P 868 " --> pdb=" O GLY P 864 " (cutoff:3.500A) Processing helix chain 'P' and resid 890 through 899 Processing helix chain 'P' and resid 923 through 927 removed outlier: 3.572A pdb=" N SER P 927 " --> pdb=" O ASP P 924 " (cutoff:3.500A) Processing helix chain 'P' and resid 937 through 942 removed outlier: 3.569A pdb=" N VAL P 940 " --> pdb=" O GLU P 937 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA P 941 " --> pdb=" O GLU P 938 " (cutoff:3.500A) Processing helix chain 'P' and resid 948 through 952 Processing helix chain 'O' and resid 89 through 104 removed outlier: 4.955A pdb=" N LEU O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 111 Processing helix chain 'O' and resid 134 through 147 Processing helix chain 'O' and resid 148 through 159 removed outlier: 3.845A pdb=" N GLN O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG O 159 " --> pdb=" O GLN O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 262 through 270 removed outlier: 4.377A pdb=" N GLN O 268 " --> pdb=" O ARG O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 284 removed outlier: 3.708A pdb=" N GLY O 283 " --> pdb=" O ASN O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 311 removed outlier: 4.162A pdb=" N GLN O 297 " --> pdb=" O ASN O 293 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE O 299 " --> pdb=" O VAL O 295 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR O 302 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET O 303 " --> pdb=" O PHE O 299 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU O 304 " --> pdb=" O ARG O 300 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU O 308 " --> pdb=" O LEU O 304 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS O 309 " --> pdb=" O GLN O 305 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'N' and resid 852 through 854 removed outlier: 4.247A pdb=" N LEU N 868 " --> pdb=" O ASP N 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 924 through 927 Processing sheet with id=AA3, first strand: chain 'N' and resid 962 through 963 Processing sheet with id=AA4, first strand: chain 'P' and resid 93 through 97 removed outlier: 3.699A pdb=" N VAL P 151 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 158 through 163 removed outlier: 3.574A pdb=" N GLU P 173 " --> pdb=" O PHE P 186 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE P 185 " --> pdb=" O SER P 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 215 through 217 Processing sheet with id=AA7, first strand: chain 'P' and resid 227 through 232 Processing sheet with id=AA8, first strand: chain 'P' and resid 299 through 305 removed outlier: 3.765A pdb=" N ILE P 299 " --> pdb=" O SER P 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA P 309 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 325 " --> pdb=" O ALA P 309 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL P 322 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY P 366 " --> pdb=" O VAL P 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 395 through 396 removed outlier: 3.769A pdb=" N ALA P 410 " --> pdb=" O LEU P 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 438 through 442 removed outlier: 3.562A pdb=" N LEU P 439 " --> pdb=" O GLN P 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 527 through 530 removed outlier: 3.719A pdb=" N GLN P 527 " --> pdb=" O VAL P 540 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE P 537 " --> pdb=" O VAL P 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 956 through 958 Processing sheet with id=AB4, first strand: chain 'X' and resid 66 through 68 368 hydrogen bonds defined for protein. 1020 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: 3.47 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4601 1.34 - 1.46: 2675 1.46 - 1.58: 6517 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13885 Sorted by residual: bond pdb=" N ASP P 556 " pdb=" CA ASP P 556 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CA VAL E 606 " pdb=" CB VAL E 606 " ideal model delta sigma weight residual 1.551 1.532 0.018 1.08e-02 8.57e+03 2.91e+00 bond pdb=" CA GLY N 800 " pdb=" C GLY N 800 " ideal model delta sigma weight residual 1.513 1.527 -0.014 1.06e-02 8.90e+03 1.86e+00 bond pdb=" C THR O 272 " pdb=" N PRO O 273 " ideal model delta sigma weight residual 1.339 1.384 -0.044 3.40e-02 8.65e+02 1.71e+00 bond pdb=" C PHE P 916 " pdb=" N PRO P 917 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.56e+00 ... (remaining 13880 not shown) Histogram of bond angle deviations from ideal: 98.93 - 106.00: 366 106.00 - 113.07: 7578 113.07 - 120.14: 4986 120.14 - 127.22: 5802 127.22 - 134.29: 166 Bond angle restraints: 18898 Sorted by residual: angle pdb=" N PRO E 254 " pdb=" CA PRO E 254 " pdb=" CB PRO E 254 " ideal model delta sigma weight residual 103.25 111.61 -8.36 1.05e+00 9.07e-01 6.34e+01 angle pdb=" N PRO P 380 " pdb=" CA PRO P 380 " pdb=" CB PRO P 380 " ideal model delta sigma weight residual 103.25 111.18 -7.93 1.05e+00 9.07e-01 5.71e+01 angle pdb=" N PRO P 869 " pdb=" CA PRO P 869 " pdb=" CB PRO P 869 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.56e+01 angle pdb=" N PRO E 305 " pdb=" CA PRO E 305 " pdb=" CB PRO E 305 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 angle pdb=" N PRO O 188 " pdb=" CA PRO O 188 " pdb=" CB PRO O 188 " ideal model delta sigma weight residual 102.86 110.55 -7.69 1.23e+00 6.61e-01 3.91e+01 ... (remaining 18893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7457 17.48 - 34.96: 773 34.96 - 52.44: 125 52.44 - 69.93: 20 69.93 - 87.41: 12 Dihedral angle restraints: 8387 sinusoidal: 3141 harmonic: 5246 Sorted by residual: dihedral pdb=" CA GLY P 487 " pdb=" C GLY P 487 " pdb=" N THR P 488 " pdb=" CA THR P 488 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU E 472 " pdb=" C LEU E 472 " pdb=" N PRO E 473 " pdb=" CA PRO E 473 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PRO P 271 " pdb=" C PRO P 271 " pdb=" N GLN P 272 " pdb=" CA GLN P 272 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 8384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1727 0.055 - 0.110: 411 0.110 - 0.165: 54 0.165 - 0.220: 7 0.220 - 0.276: 4 Chirality restraints: 2203 Sorted by residual: chirality pdb=" CA PRO E 254 " pdb=" N PRO E 254 " pdb=" C PRO E 254 " pdb=" CB PRO E 254 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN P 899 " pdb=" N ASN P 899 " pdb=" C ASN P 899 " pdb=" CB ASN P 899 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO P 380 " pdb=" N PRO P 380 " pdb=" C PRO P 380 " pdb=" CB PRO P 380 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2200 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 791 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP E 791 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 791 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 791 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 791 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 791 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 791 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 95 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C LEU O 95 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU O 95 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN O 96 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 899 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO P 900 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO P 900 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO P 900 " 0.035 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 311 2.67 - 3.23: 13340 3.23 - 3.79: 17977 3.79 - 4.34: 23283 4.34 - 4.90: 38487 Nonbonded interactions: 93398 Sorted by model distance: nonbonded pdb=" OH TYR E 402 " pdb=" OG SER E 456 " model vdw 2.115 2.440 nonbonded pdb=" OD1 ASP E 530 " pdb=" OH TYR E 583 " model vdw 2.149 2.440 nonbonded pdb=" NE2 GLN P 413 " pdb=" OE1 GLN P 438 " model vdw 2.188 2.520 nonbonded pdb=" NZ LYS P 607 " pdb=" O GLN P 635 " model vdw 2.230 2.520 nonbonded pdb=" OE1 GLN O 268 " pdb=" OG SER O 282 " model vdw 2.237 2.440 ... (remaining 93393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.150 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.060 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.004 0.053 13885 Z= 0.257 Angle : 0.828 13.987 18898 Z= 0.462 Chirality : 0.048 0.276 2203 Planarity : 0.005 0.062 2478 Dihedral : 14.636 87.407 4967 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.58 % Allowed : 19.25 % Favored : 80.16 % Rotamer: Outliers : 0.07 % Allowed : 9.67 % Favored : 90.26 % 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: -5.81 (0.16), residues: 1714 helix: -3.09 (0.16), residues: 616 sheet: -2.81 (0.35), residues: 175 loop : -4.85 (0.16), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 791 HIS 0.006 0.001 HIS E 340 PHE 0.020 0.002 PHE E 404 TYR 0.017 0.001 TYR E 343 ARG 0.010 0.000 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 PHE cc_start: 0.7552 (p90) cc_final: 0.6881 (p90) REVERT: N 870 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7900 (mmmt) REVERT: N 880 ARG cc_start: 0.6938 (mmt180) cc_final: 0.6396 (mmt90) REVERT: P 201 TRP cc_start: 0.8027 (p-90) cc_final: 0.7753 (p-90) REVERT: P 408 LEU cc_start: 0.8677 (pp) cc_final: 0.8437 (pp) REVERT: P 436 PHE cc_start: 0.6901 (m-80) cc_final: 0.6401 (m-80) REVERT: P 491 TYR cc_start: 0.6858 (t80) cc_final: 0.6617 (t80) REVERT: P 768 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8035 (ppt170) REVERT: P 904 PHE cc_start: 0.8275 (m-80) cc_final: 0.8006 (m-80) REVERT: O 144 GLN cc_start: 0.7911 (mt0) cc_final: 0.7556 (tt0) REVERT: O 264 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7430 (ttm170) REVERT: O 309 LYS cc_start: 0.8196 (mttt) cc_final: 0.7979 (mttm) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.3298 time to fit residues: 101.6390 Evaluate side-chains 181 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 644 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 369 ASN E 450 GLN E 485 GLN E 543 HIS E 618 GLN E 888 ASN ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 879 ASN P 168 HIS P 190 GLN ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 659 GLN ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 861 HIS O 297 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13885 Z= 0.220 Angle : 0.746 11.372 18898 Z= 0.377 Chirality : 0.045 0.233 2203 Planarity : 0.005 0.064 2478 Dihedral : 6.607 38.576 1909 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 18.44 % Favored : 81.33 % Rotamer: Outliers : 2.63 % Allowed : 16.70 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.90 (0.18), residues: 1714 helix: -2.30 (0.19), residues: 621 sheet: -2.42 (0.36), residues: 188 loop : -4.31 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 791 HIS 0.008 0.001 HIS P 168 PHE 0.026 0.002 PHE N 981 TYR 0.028 0.002 TYR N 891 ARG 0.006 0.000 ARG P 777 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 960 LYS cc_start: 0.7105 (mptt) cc_final: 0.6762 (mppt) REVERT: P 241 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7517 (pp) REVERT: P 325 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8089 (tm-30) REVERT: P 408 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8384 (pp) REVERT: P 491 TYR cc_start: 0.6948 (t80) cc_final: 0.6539 (t80) REVERT: P 637 MET cc_start: 0.8197 (ppp) cc_final: 0.7567 (ppp) REVERT: P 638 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (mtm110) REVERT: P 743 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7525 (mmm-85) REVERT: P 768 ARG cc_start: 0.8419 (ptp-110) cc_final: 0.7890 (ppt170) REVERT: O 144 GLN cc_start: 0.7895 (mt0) cc_final: 0.7484 (tt0) REVERT: O 309 LYS cc_start: 0.8166 (mttt) cc_final: 0.7858 (mttm) outliers start: 37 outliers final: 19 residues processed: 214 average time/residue: 0.3152 time to fit residues: 92.7586 Evaluate side-chains 204 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 304 ASN Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 430 LYS Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 chunk 135 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 161 optimal weight: 0.0000 chunk 55 optimal weight: 0.0050 chunk 130 optimal weight: 0.0570 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13885 Z= 0.199 Angle : 0.716 9.208 18898 Z= 0.362 Chirality : 0.044 0.247 2203 Planarity : 0.005 0.065 2478 Dihedral : 6.247 39.298 1909 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.39 % Favored : 82.32 % Rotamer: Outliers : 3.62 % Allowed : 18.83 % Favored : 77.54 % 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: -4.47 (0.19), residues: 1714 helix: -1.81 (0.20), residues: 618 sheet: -2.16 (0.39), residues: 165 loop : -4.14 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP P 201 HIS 0.008 0.001 HIS P 752 PHE 0.036 0.002 PHE E 223 TYR 0.026 0.001 TYR N 891 ARG 0.008 0.000 ARG O 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 66 ARG cc_start: 0.6283 (mtp85) cc_final: 0.4948 (mtp85) REVERT: E 401 MET cc_start: 0.7337 (tmm) cc_final: 0.7047 (tmm) REVERT: E 784 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7492 (p0) REVERT: N 880 ARG cc_start: 0.6682 (mmt180) cc_final: 0.6322 (mmt90) REVERT: P 241 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7377 (pp) REVERT: P 325 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7858 (tm-30) REVERT: P 408 LEU cc_start: 0.8685 (pp) cc_final: 0.8430 (pp) REVERT: P 637 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: P 638 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7846 (mtm110) REVERT: P 743 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: P 768 ARG cc_start: 0.8352 (ptp-110) cc_final: 0.7850 (ppt170) REVERT: O 144 GLN cc_start: 0.7926 (mt0) cc_final: 0.7629 (tt0) REVERT: O 264 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7200 (ttm170) REVERT: O 297 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8190 (pp30) REVERT: O 309 LYS cc_start: 0.8129 (mttt) cc_final: 0.7836 (mttm) outliers start: 51 outliers final: 29 residues processed: 237 average time/residue: 0.2904 time to fit residues: 97.1242 Evaluate side-chains 219 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 784 ASP Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 430 LYS Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 163 optimal weight: 0.2980 chunk 173 optimal weight: 0.0010 chunk 85 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13885 Z= 0.201 Angle : 0.715 9.112 18898 Z= 0.360 Chirality : 0.044 0.261 2203 Planarity : 0.005 0.066 2478 Dihedral : 6.112 40.194 1909 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.57 % Favored : 83.14 % Rotamer: Outliers : 4.76 % Allowed : 20.40 % Favored : 74.84 % 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: -4.31 (0.19), residues: 1714 helix: -1.62 (0.21), residues: 626 sheet: -2.03 (0.39), residues: 170 loop : -4.13 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP P 201 HIS 0.006 0.001 HIS P 752 PHE 0.025 0.002 PHE E 223 TYR 0.024 0.001 TYR N 896 ARG 0.007 0.000 ARG P 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 193 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 401 MET cc_start: 0.7458 (tmm) cc_final: 0.7156 (tmm) REVERT: N 880 ARG cc_start: 0.6699 (mmt180) cc_final: 0.6170 (mmt90) REVERT: P 241 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7350 (pp) REVERT: P 325 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7833 (tm-30) REVERT: P 408 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (pp) REVERT: P 494 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7781 (pmt-80) REVERT: P 637 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7483 (ppp) REVERT: P 638 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7913 (mtm110) REVERT: P 768 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.7850 (ppt170) REVERT: P 944 GLU cc_start: 0.6874 (tp30) cc_final: 0.6439 (tp30) REVERT: O 144 GLN cc_start: 0.7833 (mt0) cc_final: 0.7452 (tt0) REVERT: O 264 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7141 (ttm170) REVERT: O 309 LYS cc_start: 0.8189 (mttt) cc_final: 0.7867 (mttp) outliers start: 67 outliers final: 36 residues processed: 238 average time/residue: 0.2803 time to fit residues: 93.7921 Evaluate side-chains 227 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 763 ILE Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 193 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 367 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 494 ARG Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 267 MET Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 128 optimal weight: 0.0770 chunk 71 optimal weight: 0.3980 chunk 147 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13885 Z= 0.204 Angle : 0.718 9.663 18898 Z= 0.362 Chirality : 0.045 0.262 2203 Planarity : 0.005 0.067 2478 Dihedral : 6.043 41.050 1909 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.27 % Favored : 82.44 % Rotamer: Outliers : 4.19 % Allowed : 21.68 % Favored : 74.13 % 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: -4.16 (0.19), residues: 1714 helix: -1.50 (0.21), residues: 631 sheet: -1.95 (0.39), residues: 172 loop : -4.05 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 201 HIS 0.006 0.001 HIS P 752 PHE 0.037 0.002 PHE E 223 TYR 0.025 0.001 TYR N 896 ARG 0.008 0.000 ARG P 777 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 190 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 ASP cc_start: 0.6831 (m-30) cc_final: 0.6583 (m-30) REVERT: E 401 MET cc_start: 0.7482 (tmm) cc_final: 0.7165 (tmm) REVERT: N 869 GLU cc_start: 0.7072 (tm-30) cc_final: 0.5081 (tm-30) REVERT: N 880 ARG cc_start: 0.6617 (mmt180) cc_final: 0.5733 (mmt90) REVERT: P 241 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7382 (pp) REVERT: P 325 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7848 (tm-30) REVERT: P 408 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8393 (pp) REVERT: P 491 TYR cc_start: 0.6387 (t80) cc_final: 0.5984 (t80) REVERT: P 637 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7453 (ppp) REVERT: P 638 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (mtm110) REVERT: P 768 ARG cc_start: 0.8316 (ptp-110) cc_final: 0.7837 (ppt170) REVERT: P 944 GLU cc_start: 0.6899 (tp30) cc_final: 0.6482 (tp30) REVERT: O 144 GLN cc_start: 0.7849 (mt0) cc_final: 0.7485 (tt0) REVERT: O 264 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7145 (ttm170) REVERT: O 309 LYS cc_start: 0.8104 (mttt) cc_final: 0.7822 (mttp) outliers start: 59 outliers final: 42 residues processed: 225 average time/residue: 0.2864 time to fit residues: 90.8291 Evaluate side-chains 229 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 193 ASN Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 304 ASN Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 367 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 285 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13885 Z= 0.364 Angle : 0.823 14.967 18898 Z= 0.414 Chirality : 0.048 0.292 2203 Planarity : 0.006 0.064 2478 Dihedral : 6.608 42.335 1909 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.41 % Allowed : 19.49 % Favored : 80.11 % Rotamer: Outliers : 4.90 % Allowed : 21.75 % Favored : 73.35 % 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: -4.33 (0.19), residues: 1714 helix: -1.69 (0.20), residues: 636 sheet: -2.05 (0.38), residues: 185 loop : -4.14 (0.18), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 201 HIS 0.022 0.002 HIS P 589 PHE 0.027 0.002 PHE E 223 TYR 0.024 0.002 TYR N 896 ARG 0.009 0.001 ARG P 777 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 185 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 ARG cc_start: 0.6352 (mtp85) cc_final: 0.5024 (mtp85) REVERT: P 241 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7718 (pp) REVERT: P 304 ASN cc_start: 0.8437 (p0) cc_final: 0.8164 (p0) REVERT: P 325 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8129 (tm-30) REVERT: P 408 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8085 (pp) REVERT: P 436 PHE cc_start: 0.6779 (m-80) cc_final: 0.6489 (m-80) REVERT: P 637 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7566 (ppp) REVERT: P 638 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8096 (mtm110) REVERT: P 768 ARG cc_start: 0.8505 (ptp-110) cc_final: 0.7872 (ppt170) REVERT: P 944 GLU cc_start: 0.7083 (tp30) cc_final: 0.6692 (tp30) REVERT: O 144 GLN cc_start: 0.7979 (mt0) cc_final: 0.7686 (tt0) REVERT: O 267 MET cc_start: 0.7648 (mtp) cc_final: 0.7219 (mtp) REVERT: O 309 LYS cc_start: 0.8107 (mttt) cc_final: 0.7650 (mttm) outliers start: 69 outliers final: 50 residues processed: 230 average time/residue: 0.2797 time to fit residues: 91.2882 Evaluate side-chains 234 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 977 GLU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 367 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 494 ARG Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 chunk 98 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 105 optimal weight: 0.0270 chunk 79 optimal weight: 0.3980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS P 232 GLN ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN P 475 GLN P 589 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13885 Z= 0.191 Angle : 0.729 11.440 18898 Z= 0.366 Chirality : 0.044 0.257 2203 Planarity : 0.005 0.071 2478 Dihedral : 6.133 43.062 1909 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.28 % Favored : 83.43 % Rotamer: Outliers : 3.98 % Allowed : 23.67 % Favored : 72.35 % 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: -3.96 (0.19), residues: 1714 helix: -1.32 (0.21), residues: 633 sheet: -1.86 (0.40), residues: 170 loop : -3.95 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 201 HIS 0.006 0.001 HIS P 752 PHE 0.038 0.002 PHE E 223 TYR 0.044 0.001 TYR P 491 ARG 0.010 0.000 ARG P 777 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 195 time to evaluate : 1.459 Fit side-chains REVERT: E 70 ASP cc_start: 0.6911 (m-30) cc_final: 0.6711 (m-30) REVERT: E 401 MET cc_start: 0.7346 (tmm) cc_final: 0.7133 (tmm) REVERT: E 474 PRO cc_start: 0.6981 (Cg_exo) cc_final: 0.6742 (Cg_endo) REVERT: P 201 TRP cc_start: 0.8046 (p-90) cc_final: 0.7603 (p-90) REVERT: P 232 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6188 (mm-40) REVERT: P 241 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7361 (pp) REVERT: P 408 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8399 (pp) REVERT: P 637 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7491 (ppp) REVERT: P 644 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6570 (m-10) REVERT: P 768 ARG cc_start: 0.8295 (ptp-110) cc_final: 0.7850 (ppt170) REVERT: O 144 GLN cc_start: 0.7878 (mt0) cc_final: 0.7606 (tt0) REVERT: O 264 ARG cc_start: 0.7423 (mtt180) cc_final: 0.7053 (ttm170) REVERT: O 267 MET cc_start: 0.7528 (mtp) cc_final: 0.7050 (mtp) REVERT: O 309 LYS cc_start: 0.7880 (mttt) cc_final: 0.7471 (mttm) outliers start: 56 outliers final: 41 residues processed: 230 average time/residue: 0.2774 time to fit residues: 90.4500 Evaluate side-chains 231 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 232 GLN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS P 752 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13885 Z= 0.215 Angle : 0.744 12.060 18898 Z= 0.372 Chirality : 0.045 0.271 2203 Planarity : 0.005 0.062 2478 Dihedral : 6.059 43.654 1909 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 16.63 % Favored : 83.02 % Rotamer: Outliers : 4.05 % Allowed : 24.02 % Favored : 71.93 % 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: -3.90 (0.20), residues: 1714 helix: -1.26 (0.21), residues: 635 sheet: -1.75 (0.40), residues: 170 loop : -3.94 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 245 HIS 0.010 0.001 HIS P 589 PHE 0.029 0.002 PHE P 911 TYR 0.029 0.001 TYR N 896 ARG 0.013 0.000 ARG P 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 188 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: E 70 ASP cc_start: 0.6990 (m-30) cc_final: 0.6789 (m-30) REVERT: N 880 ARG cc_start: 0.6531 (mmt180) cc_final: 0.6200 (mmt90) REVERT: P 201 TRP cc_start: 0.8058 (p-90) cc_final: 0.7483 (p-90) REVERT: P 241 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7005 (pp) REVERT: P 408 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8395 (pp) REVERT: P 637 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7494 (ppp) REVERT: P 644 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6618 (m-10) REVERT: P 768 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.7845 (ppt170) REVERT: P 944 GLU cc_start: 0.6960 (tp30) cc_final: 0.6646 (tp30) REVERT: O 144 GLN cc_start: 0.7833 (mt0) cc_final: 0.7576 (tt0) REVERT: O 264 ARG cc_start: 0.7422 (mtt180) cc_final: 0.7055 (ttm170) REVERT: O 267 MET cc_start: 0.7537 (mtp) cc_final: 0.7047 (mtp) REVERT: O 309 LYS cc_start: 0.7754 (mttt) cc_final: 0.7311 (mttp) outliers start: 57 outliers final: 47 residues processed: 225 average time/residue: 0.2853 time to fit residues: 90.3429 Evaluate side-chains 237 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 367 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 947 LEU Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 160 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 70 optimal weight: 0.0670 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 145 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 170 optimal weight: 0.3980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS P 232 GLN ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 752 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13885 Z= 0.194 Angle : 0.729 11.247 18898 Z= 0.363 Chirality : 0.044 0.287 2203 Planarity : 0.005 0.071 2478 Dihedral : 5.842 44.046 1909 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.51 % Favored : 83.26 % Rotamer: Outliers : 4.12 % Allowed : 23.88 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.20), residues: 1714 helix: -1.14 (0.21), residues: 636 sheet: -1.65 (0.40), residues: 168 loop : -3.84 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 245 HIS 0.007 0.001 HIS P 752 PHE 0.023 0.001 PHE E 223 TYR 0.031 0.001 TYR N 896 ARG 0.009 0.000 ARG P 743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 191 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: E 401 MET cc_start: 0.7330 (tmm) cc_final: 0.7118 (tmm) REVERT: E 474 PRO cc_start: 0.7083 (Cg_exo) cc_final: 0.6850 (Cg_endo) REVERT: E 493 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6579 (ptt-90) REVERT: N 880 ARG cc_start: 0.6380 (mmt180) cc_final: 0.5826 (mmt90) REVERT: P 201 TRP cc_start: 0.7953 (p-90) cc_final: 0.7625 (p-90) REVERT: P 241 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6984 (pp) REVERT: P 408 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8366 (pp) REVERT: P 409 TYR cc_start: 0.6136 (p90) cc_final: 0.4767 (p90) REVERT: P 637 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7557 (ppp) REVERT: P 644 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6601 (m-10) REVERT: P 768 ARG cc_start: 0.8271 (ptp-110) cc_final: 0.7825 (ppt170) REVERT: P 944 GLU cc_start: 0.6909 (tp30) cc_final: 0.6593 (tp30) REVERT: O 267 MET cc_start: 0.7517 (mtp) cc_final: 0.7060 (mtp) REVERT: O 309 LYS cc_start: 0.7652 (mttt) cc_final: 0.7400 (mttp) outliers start: 58 outliers final: 45 residues processed: 231 average time/residue: 0.2755 time to fit residues: 90.5238 Evaluate side-chains 231 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 574 LEU Chi-restraints excluded: chain P residue 588 ILE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 947 LEU Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 0.0870 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 752 HIS ** P 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13885 Z= 0.306 Angle : 0.800 15.147 18898 Z= 0.397 Chirality : 0.047 0.246 2203 Planarity : 0.005 0.064 2478 Dihedral : 6.227 44.529 1909 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.41 % Allowed : 18.26 % Favored : 81.33 % Rotamer: Outliers : 4.05 % Allowed : 23.95 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1714 helix: -1.26 (0.21), residues: 635 sheet: -1.68 (0.40), residues: 167 loop : -3.92 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 201 HIS 0.008 0.001 HIS P 433 PHE 0.030 0.002 PHE E 447 TYR 0.027 0.002 TYR N 896 ARG 0.010 0.001 ARG P 777 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 181 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 66 ARG cc_start: 0.6398 (mtp85) cc_final: 0.5090 (mtp85) REVERT: E 493 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6621 (ptt-90) REVERT: N 880 ARG cc_start: 0.6643 (mmt180) cc_final: 0.6220 (mmt90) REVERT: P 201 TRP cc_start: 0.7936 (p-90) cc_final: 0.7431 (p-90) REVERT: P 241 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7785 (pp) REVERT: P 325 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7945 (tm-30) REVERT: P 408 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8144 (pp) REVERT: P 637 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7485 (ppp) REVERT: P 644 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6596 (m-10) REVERT: P 768 ARG cc_start: 0.8394 (ptp-110) cc_final: 0.7892 (ptm160) REVERT: P 944 GLU cc_start: 0.6931 (tp30) cc_final: 0.6615 (tp30) REVERT: O 267 MET cc_start: 0.7567 (mtp) cc_final: 0.7105 (mtp) REVERT: O 309 LYS cc_start: 0.7779 (mttt) cc_final: 0.7450 (mttm) outliers start: 57 outliers final: 50 residues processed: 223 average time/residue: 0.2882 time to fit residues: 91.1417 Evaluate side-chains 235 residues out of total 1503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 493 ARG Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 263 ASN Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 358 ASP Chi-restraints excluded: chain P residue 367 ASP Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 588 ILE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 626 ASP Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 911 PHE Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 947 LEU Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.6980 chunk 130 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 142 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 210 HIS ** P 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 752 HIS ** P 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094746 restraints weight = 38855.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.096892 restraints weight = 21007.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098284 restraints weight = 13915.173| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13885 Z= 0.193 Angle : 0.744 12.515 18898 Z= 0.369 Chirality : 0.044 0.257 2203 Planarity : 0.005 0.071 2478 Dihedral : 5.890 44.890 1909 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.28 % Favored : 83.49 % Rotamer: Outliers : 3.55 % Allowed : 24.52 % Favored : 71.93 % 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: -3.65 (0.20), residues: 1714 helix: -1.13 (0.21), residues: 647 sheet: -1.58 (0.41), residues: 158 loop : -3.73 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 245 HIS 0.011 0.001 HIS P 760 PHE 0.030 0.001 PHE E 447 TYR 0.032 0.001 TYR N 896 ARG 0.009 0.000 ARG P 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3109.59 seconds wall clock time: 56 minutes 38.59 seconds (3398.59 seconds total)