Starting phenix.real_space_refine on Wed Aug 7 02:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b61_44234/08_2024/9b61_44234.cif" } resolution = 2.81 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= 0.000 sd= 0.001 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 128 5.16 5 C 12003 2.51 5 N 2954 2.21 5 O 3362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 5": "OD1" <-> "OD2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 688": "OE1" <-> "OE2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 728": "OD1" <-> "OD2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "D TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 782": "OE1" <-> "OE2" Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 203": "OD1" <-> "OD2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18447 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3116 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 404, 3116 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3166 Chain: "B" Number of atoms: 3178 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3167 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 411, 3167 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3223 Chain: "A" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3109 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 3181 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 411, 3165 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Conformer: "B" Number of residues, atoms: 411, 3165 Classifications: {'peptide': 411} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 397} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 bond proxies already assigned to first conformer: 3216 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.42 residue: pdb=" N APHE B 623 " occ=0.34 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.66 residue: pdb=" N APHE D 623 " occ=0.51 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.49 Time building chain proxies: 14.57, per 1000 atoms: 0.79 Number of scatterers: 18447 At special positions: 0 Unit cell: (113.16, 111.52, 146.78, 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 128 16.00 O 3362 8.00 N 2954 7.00 C 12003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 5.3 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4378 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 60.8% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.535A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.080A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 4.045A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.562A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 132 through 162 removed outlier: 4.091A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 416 through 419 removed outlier: 4.034A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.959A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.524A pdb=" N GLY C 465 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 468 " --> pdb=" O VAL C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.751A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 519 " --> pdb=" O SER C 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 515 through 519' Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.540A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.895A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.756A pdb=" N LYS C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 672 " --> pdb=" O ASP C 668 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR C 673 " --> pdb=" O LYS C 669 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 removed outlier: 3.614A pdb=" N LYS C 695 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 715 removed outlier: 3.507A pdb=" N GLU C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.602A pdb=" N VAL C 746 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 removed outlier: 3.587A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.562A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.078A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.743A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 4.016A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 removed outlier: 4.024A pdb=" N TRP B 551 " --> pdb=" O PRO B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.672A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 3.687A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.659A pdb=" N VAL B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.710A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.507A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.738A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.952A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.802A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 675 removed outlier: 4.314A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP A 671 " --> pdb=" O PHE A 667 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.507A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 769 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.722A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.721A pdb=" N GLU D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 489 removed outlier: 3.797A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 4.022A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 removed outlier: 3.543A pdb=" N TRP D 551 " --> pdb=" O PRO D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 675 removed outlier: 3.581A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.667A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.556A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 753 removed outlier: 3.623A pdb=" N VAL D 746 " --> pdb=" O LEU D 742 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 769 Processing helix chain 'D' and resid 788 through 825 removed outlier: 3.838A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 161 Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.539A pdb=" N PHE E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 209 " --> pdb=" O HIS E 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 30 removed outlier: 3.723A pdb=" N GLN G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.922A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.532A pdb=" N LEU G 185 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 187 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.533A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.724A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 3.713A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR C 398 " --> pdb=" O ILE C 474 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 407 through 408 removed outlier: 4.104A pdb=" N GLU C 422 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.612A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 502 through 505 removed outlier: 4.422A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.698A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 440 through 444 removed outlier: 5.834A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 476 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 398 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 440 through 444 removed outlier: 5.834A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 476 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 398 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.507A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.121A pdb=" N VAL A 396 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.862A pdb=" N GLU A 422 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 489 through 498 removed outlier: 4.642A pdb=" N ILE A 734 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 732 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET A 496 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS A 730 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.684A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 503 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.931A pdb=" N ILE D 474 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.931A pdb=" N ILE D 474 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA D 477 " --> pdb=" O ASP D 733 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASP D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU D 479 " --> pdb=" O GLY D 731 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 731 " --> pdb=" O LEU D 479 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.636A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.636A pdb=" N LYS E 78 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR E 66 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 79 1144 hydrogen bonds defined for protein. 3349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 2 1.21 - 1.36: 5719 1.36 - 1.51: 6074 1.51 - 1.67: 6860 1.67 - 1.82: 208 Bond restraints: 18863 Sorted by residual: bond pdb=" CG PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 1.503 1.173 0.330 3.40e-02 8.65e+02 9.41e+01 bond pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 1.492 1.052 0.440 5.00e-02 4.00e+02 7.74e+01 bond pdb=" CG PRO B 478 " pdb=" CD PRO B 478 " ideal model delta sigma weight residual 1.503 1.413 0.090 3.40e-02 8.65e+02 7.06e+00 bond pdb=" N PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 1.473 1.510 -0.037 1.40e-02 5.10e+03 7.04e+00 bond pdb=" CA PRO A 745 " pdb=" CB PRO A 745 " ideal model delta sigma weight residual 1.534 1.557 -0.024 1.49e-02 4.50e+03 2.49e+00 ... (remaining 18858 not shown) Histogram of bond angle deviations from ideal: 76.27 - 94.28: 4 94.28 - 112.30: 9672 112.30 - 130.32: 15765 130.32 - 148.34: 81 148.34 - 166.35: 1 Bond angle restraints: 25523 Sorted by residual: angle pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 106.10 166.35 -60.25 3.20e+00 9.77e-02 3.55e+02 angle pdb=" N PRO A 745 " pdb=" CD PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 103.20 76.27 26.93 1.50e+00 4.44e-01 3.22e+02 angle pdb=" CA PRO A 745 " pdb=" CB PRO A 745 " pdb=" CG PRO A 745 " ideal model delta sigma weight residual 104.50 76.91 27.59 1.90e+00 2.77e-01 2.11e+02 angle pdb=" CA PRO A 745 " pdb=" N PRO A 745 " pdb=" CD PRO A 745 " ideal model delta sigma weight residual 112.00 102.04 9.96 1.40e+00 5.10e-01 5.06e+01 angle pdb=" N PRO B 478 " pdb=" CD PRO B 478 " pdb=" CG PRO B 478 " ideal model delta sigma weight residual 103.20 93.71 9.49 1.50e+00 4.44e-01 4.01e+01 ... (remaining 25518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 9362 17.57 - 35.15: 1213 35.15 - 52.72: 359 52.72 - 70.29: 58 70.29 - 87.86: 25 Dihedral angle restraints: 11017 sinusoidal: 4159 harmonic: 6858 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 168.87 -75.87 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 137.68 -44.68 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS G 67 " pdb=" SG CYS G 67 " pdb=" SG CYS G 77 " pdb=" CB CYS G 77 " ideal model delta sinusoidal sigma weight residual -86.00 -129.24 43.24 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 11014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1923 0.033 - 0.066: 696 0.066 - 0.099: 190 0.099 - 0.132: 67 0.132 - 0.165: 7 Chirality restraints: 2883 Sorted by residual: chirality pdb=" CA ASP E 86 " pdb=" N ASP E 86 " pdb=" C ASP E 86 " pdb=" CB ASP E 86 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CG LEU H 115 " pdb=" CB LEU H 115 " pdb=" CD1 LEU H 115 " pdb=" CD2 LEU H 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2880 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.054 5.00e-02 4.00e+02 7.78e-02 9.69e+00 pdb=" N PRO B 478 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 671 " 0.012 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP A 671 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 671 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 671 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 671 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 671 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 671 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 671 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 671 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 671 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 819 " -0.189 9.50e-02 1.11e+02 8.56e-02 5.93e+00 pdb=" NE ARG C 819 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG C 819 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 819 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 819 " 0.000 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 489 2.70 - 3.25: 18839 3.25 - 3.80: 31542 3.80 - 4.35: 38218 4.35 - 4.90: 63587 Nonbonded interactions: 152675 Sorted by model distance: nonbonded pdb=" OE1 GLU C 524 " pdb=" OH TYR G 176 " model vdw 2.154 3.040 nonbonded pdb=" N GLU C 637 " pdb=" OE1 GLU C 637 " model vdw 2.190 3.120 nonbonded pdb=" N GLN B 508 " pdb=" OE1 GLN B 508 " model vdw 2.211 3.120 nonbonded pdb=" N GLU A 705 " pdb=" OE1 GLU A 705 " model vdw 2.213 3.120 nonbonded pdb=" OE1 GLU A 524 " pdb=" OH TYR E 176 " model vdw 2.232 3.040 ... (remaining 152670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 6 \ 83 or (resid 684 and (name N or name CA or name C or name O or name CB )) or res \ id 685 through 763 or resid 765 through 812 or (resid 813 and (name N or name CA \ or name C or name O or name CB )) or resid 814 through 818 or (resid 819 throug \ h 820 and (name N or name CA or name C or name O or name CB )) or resid 821 thro \ ugh 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 760 or (resid 761 and (name N or name CA or name \ C or name O or name CB )) or resid 762 through 763 or (resid 765 and (name N or \ name CA or name C or name O or name CB )) or resid 766 through 773 or (resid 784 \ and (name N or name CA or name C or name O or name CB )) or resid 785 through 8 \ 25)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 683 or (resid 684 and (name \ N or name CA or name C or name O or name CB )) or resid 685 through 763 or resid \ 765 through 812 or (resid 813 and (name N or name CA or name C or name O or nam \ e CB )) or resid 814 through 818 or (resid 819 through 820 and (name N or name C \ A or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 760 or (resi \ d 761 and (name N or name CA or name C or name O or name CB )) or resid 762 thro \ ugh 763 or (resid 765 and (name N or name CA or name C or name O or name CB )) o \ r resid 766 through 773 or (resid 784 and (name N or name CA or name C or name O \ or name CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.170 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.005 0.440 18863 Z= 0.370 Angle : 0.801 60.254 25523 Z= 0.373 Chirality : 0.039 0.165 2883 Planarity : 0.004 0.086 3153 Dihedral : 17.298 87.863 6603 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.10 % Allowed : 33.97 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2343 helix: 2.24 (0.14), residues: 1313 sheet: -1.27 (0.40), residues: 162 loop : -0.68 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 671 HIS 0.008 0.001 HIS F 132 PHE 0.022 0.001 PHE E 73 TYR 0.022 0.001 TYR B 673 ARG 0.021 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 ASP cc_start: 0.7765 (m-30) cc_final: 0.7432 (m-30) REVERT: F 200 MET cc_start: 0.7788 (mtt) cc_final: 0.7213 (mtt) REVERT: C 819 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6760 (ttm-80) REVERT: B 782 GLU cc_start: 0.5819 (pp20) cc_final: 0.5388 (pm20) REVERT: E 129 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8070 (mppt) outliers start: 57 outliers final: 54 residues processed: 360 average time/residue: 1.2497 time to fit residues: 508.7829 Evaluate side-chains 354 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 300 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 524 GLU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 524 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 726 ASN Chi-restraints excluded: chain A residue 773 CYS Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 699 LYS Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 205 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18863 Z= 0.217 Angle : 0.604 10.579 25523 Z= 0.304 Chirality : 0.040 0.158 2883 Planarity : 0.004 0.052 3153 Dihedral : 5.903 59.750 2641 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.29 % Allowed : 30.25 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2343 helix: 2.32 (0.14), residues: 1366 sheet: -1.51 (0.40), residues: 146 loop : -0.70 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 766 HIS 0.003 0.001 HIS E 199 PHE 0.015 0.001 PHE E 73 TYR 0.020 0.001 TYR C 424 ARG 0.012 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 327 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7617 (mtp180) REVERT: H 192 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7318 (mtt) REVERT: H 200 MET cc_start: 0.8380 (tpp) cc_final: 0.7785 (mtp) REVERT: H 204 ARG cc_start: 0.7257 (mmp-170) cc_final: 0.7043 (mmp-170) REVERT: F 31 ASP cc_start: 0.7646 (m-30) cc_final: 0.7279 (m-30) REVERT: F 134 ILE cc_start: 0.7555 (pp) cc_final: 0.7325 (pt) REVERT: F 196 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8364 (tt) REVERT: F 204 ARG cc_start: 0.7326 (mmp-170) cc_final: 0.6843 (tpm170) REVERT: C 627 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: C 674 MET cc_start: 0.8010 (pmm) cc_final: 0.7808 (pmm) REVERT: C 694 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8094 (mmt-90) REVERT: A 747 ASN cc_start: 0.8146 (m-40) cc_final: 0.7914 (m-40) REVERT: D 496 MET cc_start: 0.8204 (ptp) cc_final: 0.6989 (mtm) REVERT: D 678 GLU cc_start: 0.7481 (mm-30) cc_final: 0.6901 (mp0) REVERT: E 6 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7905 (mmm160) REVERT: E 129 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8052 (mppt) outliers start: 80 outliers final: 29 residues processed: 378 average time/residue: 1.2452 time to fit residues: 529.9946 Evaluate side-chains 333 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 301 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 211 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18863 Z= 0.265 Angle : 0.600 10.589 25523 Z= 0.302 Chirality : 0.040 0.159 2883 Planarity : 0.004 0.055 3153 Dihedral : 4.772 57.795 2578 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.03 % Allowed : 30.61 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2343 helix: 2.24 (0.14), residues: 1375 sheet: -1.44 (0.40), residues: 144 loop : -0.80 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 671 HIS 0.008 0.001 HIS G 82 PHE 0.018 0.001 PHE C 584 TYR 0.017 0.001 TYR C 424 ARG 0.011 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 320 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 14 THR cc_start: 0.8473 (m) cc_final: 0.8273 (m) REVERT: H 24 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8692 (mmm) REVERT: H 192 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7346 (mtt) REVERT: F 31 ASP cc_start: 0.7576 (m-30) cc_final: 0.7347 (m-30) REVERT: F 196 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (tt) REVERT: F 204 ARG cc_start: 0.7349 (mmp-170) cc_final: 0.6881 (tpm170) REVERT: C 408 MET cc_start: 0.5753 (tpt) cc_final: 0.5365 (tpp) REVERT: C 594 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (mtt90) REVERT: C 627 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: B 670 MET cc_start: 0.8185 (ppp) cc_final: 0.7657 (ppp) REVERT: B 708 MET cc_start: 0.8304 (tpp) cc_final: 0.7907 (tpp) REVERT: B 714 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6635 (mm-40) REVERT: B 765 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7446 (tmtm) REVERT: B 770 LYS cc_start: 0.8355 (ptmm) cc_final: 0.8151 (mptt) REVERT: A 747 ASN cc_start: 0.8211 (m-40) cc_final: 0.7979 (m-40) REVERT: A 767 TRP cc_start: 0.7430 (m-90) cc_final: 0.7161 (m-90) REVERT: D 660 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7753 (mtm-85) REVERT: D 782 GLU cc_start: 0.6948 (mp0) cc_final: 0.6670 (mp0) REVERT: E 6 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7892 (mmm160) REVERT: E 37 ARG cc_start: 0.7331 (mtp85) cc_final: 0.7031 (mtp85) REVERT: E 129 LYS cc_start: 0.8281 (mmmm) cc_final: 0.8036 (mppt) REVERT: G 11 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8033 (tm) REVERT: G 78 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7449 (ptpt) REVERT: G 206 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7748 (ttpp) outliers start: 76 outliers final: 39 residues processed: 366 average time/residue: 1.2445 time to fit residues: 512.3978 Evaluate side-chains 347 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 299 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 200 MET Chi-restraints excluded: chain G residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 0.3980 chunk 226 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN A 709 ASN A 714 GLN D 764 ASN A ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18863 Z= 0.348 Angle : 0.636 10.669 25523 Z= 0.320 Chirality : 0.042 0.164 2883 Planarity : 0.004 0.055 3153 Dihedral : 4.615 56.234 2572 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.64 % Allowed : 28.96 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2343 helix: 2.08 (0.14), residues: 1351 sheet: -1.48 (0.36), residues: 174 loop : -0.81 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 671 HIS 0.006 0.001 HIS F 205 PHE 0.020 0.002 PHE C 584 TYR 0.019 0.001 TYR G 32 ARG 0.007 0.001 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 319 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 66 THR cc_start: 0.8625 (p) cc_final: 0.8080 (t) REVERT: H 86 ASP cc_start: 0.1429 (OUTLIER) cc_final: 0.0985 (p0) REVERT: H 192 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7384 (mtt) REVERT: F 31 ASP cc_start: 0.7736 (m-30) cc_final: 0.7526 (m-30) REVERT: F 78 LYS cc_start: 0.8572 (ptmt) cc_final: 0.7885 (pttm) REVERT: F 196 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (tt) REVERT: F 204 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6894 (tpm170) REVERT: C 408 MET cc_start: 0.5840 (tpt) cc_final: 0.5452 (tpp) REVERT: C 594 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7888 (mtt90) REVERT: C 673 TYR cc_start: 0.7688 (t80) cc_final: 0.7487 (t80) REVERT: B 497 SER cc_start: 0.8449 (m) cc_final: 0.8247 (t) REVERT: B 708 MET cc_start: 0.8434 (tpp) cc_final: 0.7986 (tpp) REVERT: B 765 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7486 (tmtm) REVERT: B 782 GLU cc_start: 0.6237 (pp20) cc_final: 0.5961 (pm20) REVERT: B 783 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7316 (tptm) REVERT: A 420 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7661 (mtm110) REVERT: A 747 ASN cc_start: 0.8215 (m-40) cc_final: 0.7962 (m-40) REVERT: A 764 ASN cc_start: 0.8659 (p0) cc_final: 0.8420 (p0) REVERT: D 398 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.6092 (t) REVERT: D 496 MET cc_start: 0.8251 (ptp) cc_final: 0.7035 (mtm) REVERT: D 594 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7861 (mtp85) REVERT: D 678 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7218 (mp0) REVERT: E 6 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7853 (mmm160) REVERT: E 10 MET cc_start: 0.8287 (tpt) cc_final: 0.8084 (tpt) REVERT: E 37 ARG cc_start: 0.7322 (mtp85) cc_final: 0.6998 (mtp85) REVERT: E 99 ARG cc_start: 0.7100 (mpp80) cc_final: 0.6698 (mpp80) REVERT: E 129 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8031 (mppt) REVERT: G 11 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8168 (tm) REVERT: G 59 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6928 (t) REVERT: G 78 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7361 (ptpt) outliers start: 106 outliers final: 53 residues processed: 387 average time/residue: 1.2542 time to fit residues: 546.6059 Evaluate side-chains 362 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 298 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 594 ARG Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 765 LYS Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18863 Z= 0.177 Angle : 0.601 10.829 25523 Z= 0.294 Chirality : 0.039 0.147 2883 Planarity : 0.004 0.052 3153 Dihedral : 4.335 53.849 2571 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.93 % Allowed : 31.33 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2343 helix: 2.40 (0.14), residues: 1365 sheet: -1.38 (0.40), residues: 150 loop : -0.83 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 671 HIS 0.008 0.001 HIS F 205 PHE 0.011 0.001 PHE H 107 TYR 0.019 0.001 TYR B 549 ARG 0.008 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 326 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1598 (OUTLIER) cc_final: 0.1146 (p0) REVERT: H 192 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.7320 (mtt) REVERT: F 31 ASP cc_start: 0.7701 (m-30) cc_final: 0.7483 (m-30) REVERT: F 78 LYS cc_start: 0.8573 (ptmt) cc_final: 0.7820 (pttm) REVERT: F 196 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8365 (tt) REVERT: F 204 ARG cc_start: 0.7363 (mmp-170) cc_final: 0.6927 (tpm170) REVERT: F 206 LYS cc_start: 0.6556 (tmmt) cc_final: 0.5988 (mtpp) REVERT: C 408 MET cc_start: 0.5709 (tpt) cc_final: 0.5222 (tpp) REVERT: C 627 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: C 673 TYR cc_start: 0.7603 (t80) cc_final: 0.7377 (t80) REVERT: B 407 MET cc_start: 0.6533 (pmm) cc_final: 0.6254 (pmm) REVERT: B 500 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7416 (tp) REVERT: B 670 MET cc_start: 0.8107 (ppp) cc_final: 0.7851 (pmm) REVERT: B 674 MET cc_start: 0.7673 (pmm) cc_final: 0.6920 (pmm) REVERT: B 675 ARG cc_start: 0.7388 (mmt180) cc_final: 0.6599 (mmt180) REVERT: B 708 MET cc_start: 0.8475 (tpp) cc_final: 0.8252 (tpp) REVERT: B 782 GLU cc_start: 0.6072 (pp20) cc_final: 0.5861 (pm20) REVERT: A 764 ASN cc_start: 0.8643 (p0) cc_final: 0.8435 (p0) REVERT: A 767 TRP cc_start: 0.7406 (m-90) cc_final: 0.6965 (m-90) REVERT: D 398 THR cc_start: 0.6229 (OUTLIER) cc_final: 0.6020 (t) REVERT: D 496 MET cc_start: 0.8260 (ptp) cc_final: 0.7079 (mtm) REVERT: D 660 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7748 (mtm-85) REVERT: D 694 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: E 6 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7915 (mmm160) REVERT: E 129 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8065 (mppt) REVERT: G 11 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8141 (tm) REVERT: G 185 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7272 (mm) outliers start: 73 outliers final: 37 residues processed: 369 average time/residue: 1.2459 time to fit residues: 517.7776 Evaluate side-chains 345 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 300 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 128 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 20.0000 chunk 203 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18863 Z= 0.251 Angle : 0.623 12.574 25523 Z= 0.305 Chirality : 0.040 0.166 2883 Planarity : 0.004 0.061 3153 Dihedral : 4.388 52.562 2571 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.03 % Allowed : 31.33 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2343 helix: 2.27 (0.14), residues: 1363 sheet: -1.41 (0.37), residues: 170 loop : -0.79 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.017 0.001 PHE C 584 TYR 0.014 0.001 TYR G 32 ARG 0.015 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 308 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1618 (OUTLIER) cc_final: 0.1161 (p0) REVERT: H 99 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7621 (mtp180) REVERT: H 192 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7371 (mtt) REVERT: H 204 ARG cc_start: 0.7540 (mmm160) cc_final: 0.7191 (mmp-170) REVERT: F 31 ASP cc_start: 0.7707 (m-30) cc_final: 0.7199 (m-30) REVERT: F 65 ARG cc_start: 0.7486 (pmt170) cc_final: 0.7224 (pmt170) REVERT: F 78 LYS cc_start: 0.8554 (ptmt) cc_final: 0.7781 (pttm) REVERT: F 196 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8438 (tt) REVERT: F 204 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6861 (tpm170) REVERT: C 408 MET cc_start: 0.5754 (tpt) cc_final: 0.5257 (tpp) REVERT: C 673 TYR cc_start: 0.7740 (t80) cc_final: 0.7483 (t80) REVERT: B 670 MET cc_start: 0.8212 (ppp) cc_final: 0.7870 (pmm) REVERT: B 708 MET cc_start: 0.8547 (tpp) cc_final: 0.8227 (tpp) REVERT: A 747 ASN cc_start: 0.8306 (m-40) cc_final: 0.7983 (m-40) REVERT: A 767 TRP cc_start: 0.7434 (m-90) cc_final: 0.6983 (m-90) REVERT: D 398 THR cc_start: 0.6246 (OUTLIER) cc_final: 0.6040 (t) REVERT: D 496 MET cc_start: 0.8313 (ptp) cc_final: 0.7125 (mtm) REVERT: D 660 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7662 (mtm-85) REVERT: D 678 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7135 (mp0) REVERT: E 6 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7933 (mmm160) REVERT: G 11 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8144 (tm) REVERT: G 59 THR cc_start: 0.7247 (p) cc_final: 0.6831 (t) REVERT: G 69 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6705 (pt) REVERT: G 78 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7598 (ptpt) outliers start: 75 outliers final: 49 residues processed: 356 average time/residue: 1.2451 time to fit residues: 500.3541 Evaluate side-chains 355 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 299 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 431 GLU Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 4.9990 chunk 25 optimal weight: 0.0050 chunk 128 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 190 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 225 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18863 Z= 0.177 Angle : 0.611 10.859 25523 Z= 0.298 Chirality : 0.039 0.159 2883 Planarity : 0.004 0.053 3153 Dihedral : 4.094 51.347 2569 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.52 % Allowed : 32.16 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.18), residues: 2343 helix: 2.51 (0.14), residues: 1351 sheet: -1.25 (0.37), residues: 174 loop : -0.80 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 671 HIS 0.007 0.001 HIS F 205 PHE 0.011 0.001 PHE G 97 TYR 0.011 0.001 TYR C 424 ARG 0.010 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 311 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1710 (OUTLIER) cc_final: 0.1228 (p0) REVERT: H 192 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: H 204 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7230 (mmp-170) REVERT: H 207 GLN cc_start: 0.7794 (tp40) cc_final: 0.7558 (tt0) REVERT: F 78 LYS cc_start: 0.8571 (ptmt) cc_final: 0.7763 (pttm) REVERT: F 196 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8392 (tt) REVERT: F 204 ARG cc_start: 0.7387 (mmp-170) cc_final: 0.6875 (tpm170) REVERT: F 206 LYS cc_start: 0.6740 (tmmt) cc_final: 0.6127 (mtpp) REVERT: C 408 MET cc_start: 0.5628 (tpt) cc_final: 0.5148 (tpp) REVERT: C 673 TYR cc_start: 0.7650 (t80) cc_final: 0.7404 (t80) REVERT: C 674 MET cc_start: 0.8045 (pmm) cc_final: 0.7732 (pmm) REVERT: B 503 MET cc_start: 0.8440 (ttm) cc_final: 0.8041 (mmm) REVERT: B 670 MET cc_start: 0.8172 (ppp) cc_final: 0.7660 (pmt) REVERT: B 708 MET cc_start: 0.8555 (tpp) cc_final: 0.8119 (tpp) REVERT: A 767 TRP cc_start: 0.7323 (m-90) cc_final: 0.6866 (m-90) REVERT: D 398 THR cc_start: 0.6164 (OUTLIER) cc_final: 0.5953 (t) REVERT: D 496 MET cc_start: 0.8305 (ptp) cc_final: 0.7124 (mtm) REVERT: D 594 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: E 6 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.7907 (mmm160) REVERT: E 206 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7902 (ttmm) REVERT: G 11 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8150 (tm) REVERT: G 59 THR cc_start: 0.7120 (p) cc_final: 0.6611 (t) REVERT: G 69 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6905 (pt) REVERT: G 78 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7369 (ptpt) REVERT: G 185 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7193 (mm) outliers start: 65 outliers final: 38 residues processed: 352 average time/residue: 1.1461 time to fit residues: 456.6304 Evaluate side-chains 340 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 294 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18863 Z= 0.199 Angle : 0.643 11.416 25523 Z= 0.312 Chirality : 0.040 0.178 2883 Planarity : 0.004 0.056 3153 Dihedral : 3.795 50.767 2564 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 32.32 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2343 helix: 2.45 (0.14), residues: 1353 sheet: -1.21 (0.37), residues: 174 loop : -0.79 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 671 HIS 0.007 0.001 HIS G 60 PHE 0.012 0.001 PHE C 584 TYR 0.010 0.001 TYR C 424 ARG 0.012 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 312 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.1770 (OUTLIER) cc_final: 0.1293 (p0) REVERT: H 192 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7237 (mtt) REVERT: H 207 GLN cc_start: 0.7787 (tp40) cc_final: 0.7517 (mt0) REVERT: F 31 ASP cc_start: 0.7563 (m-30) cc_final: 0.7343 (m-30) REVERT: F 78 LYS cc_start: 0.8587 (ptmt) cc_final: 0.7809 (pttm) REVERT: F 196 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (tt) REVERT: F 204 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6890 (tpm170) REVERT: F 206 LYS cc_start: 0.6753 (tmmt) cc_final: 0.6137 (mtpp) REVERT: C 408 MET cc_start: 0.5640 (tpt) cc_final: 0.5161 (tpp) REVERT: C 463 MET cc_start: 0.7502 (mmm) cc_final: 0.6615 (mmt) REVERT: C 627 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: C 673 TYR cc_start: 0.7599 (t80) cc_final: 0.7328 (t80) REVERT: C 674 MET cc_start: 0.8084 (pmm) cc_final: 0.7817 (pmm) REVERT: B 503 MET cc_start: 0.8487 (ttm) cc_final: 0.8021 (mmm) REVERT: B 670 MET cc_start: 0.8122 (ppp) cc_final: 0.7681 (pmt) REVERT: A 767 TRP cc_start: 0.7306 (m-90) cc_final: 0.6823 (m-90) REVERT: D 398 THR cc_start: 0.6168 (OUTLIER) cc_final: 0.5960 (t) REVERT: D 496 MET cc_start: 0.8319 (ptp) cc_final: 0.7141 (mtm) REVERT: D 594 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7837 (mtp85) REVERT: D 660 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7602 (mtm-85) REVERT: E 6 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7921 (mmm160) REVERT: E 117 MET cc_start: 0.5114 (tpt) cc_final: 0.4913 (tpt) REVERT: E 206 LYS cc_start: 0.8197 (ptmt) cc_final: 0.7945 (ttpt) REVERT: G 11 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8151 (tm) REVERT: G 69 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6628 (pt) REVERT: G 185 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7255 (mm) outliers start: 68 outliers final: 44 residues processed: 350 average time/residue: 1.2048 time to fit residues: 477.0640 Evaluate side-chains 356 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 302 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 663 LYS Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 200 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN B 726 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18863 Z= 0.222 Angle : 0.663 13.640 25523 Z= 0.320 Chirality : 0.040 0.175 2883 Planarity : 0.004 0.059 3153 Dihedral : 3.844 50.517 2564 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.62 % Allowed : 32.68 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2343 helix: 2.40 (0.14), residues: 1353 sheet: -1.13 (0.37), residues: 174 loop : -0.83 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.014 0.001 PHE C 584 TYR 0.019 0.001 TYR G 156 ARG 0.008 0.001 ARG C 819 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 304 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLN cc_start: 0.7810 (pp30) cc_final: 0.7160 (mt0) REVERT: H 86 ASP cc_start: 0.1864 (OUTLIER) cc_final: 0.1385 (p0) REVERT: H 192 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7261 (mtt) REVERT: H 207 GLN cc_start: 0.7803 (tp40) cc_final: 0.7479 (mt0) REVERT: F 78 LYS cc_start: 0.8594 (ptmt) cc_final: 0.7804 (pttm) REVERT: F 204 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6955 (tpm170) REVERT: F 206 LYS cc_start: 0.6823 (tmmt) cc_final: 0.6232 (mtpp) REVERT: C 408 MET cc_start: 0.5642 (tpt) cc_final: 0.5148 (tpp) REVERT: C 463 MET cc_start: 0.7569 (mmm) cc_final: 0.6682 (mmt) REVERT: C 627 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: C 819 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6603 (tpp80) REVERT: B 407 MET cc_start: 0.6646 (pmm) cc_final: 0.5388 (pmm) REVERT: B 670 MET cc_start: 0.8017 (ppp) cc_final: 0.7611 (pmt) REVERT: B 708 MET cc_start: 0.8590 (tpp) cc_final: 0.8093 (tpp) REVERT: A 767 TRP cc_start: 0.7287 (m-90) cc_final: 0.6810 (m-90) REVERT: D 398 THR cc_start: 0.6167 (OUTLIER) cc_final: 0.5945 (t) REVERT: D 594 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7834 (mtp85) REVERT: D 660 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7624 (mtm-85) REVERT: E 6 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.7924 (mmm160) REVERT: E 117 MET cc_start: 0.5174 (tpt) cc_final: 0.4953 (tpt) REVERT: E 206 LYS cc_start: 0.8236 (ptmt) cc_final: 0.7956 (ttmm) REVERT: G 11 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8155 (tm) REVERT: G 69 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7028 (pt) REVERT: G 185 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7269 (mm) outliers start: 67 outliers final: 44 residues processed: 343 average time/residue: 1.2316 time to fit residues: 479.5569 Evaluate side-chains 347 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 594 ARG Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 10.0000 chunk 135 optimal weight: 0.0030 chunk 105 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 233 optimal weight: 0.1980 chunk 214 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 113 optimal weight: 0.0070 chunk 147 optimal weight: 8.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 149 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18863 Z= 0.175 Angle : 0.661 12.771 25523 Z= 0.319 Chirality : 0.040 0.277 2883 Planarity : 0.004 0.058 3153 Dihedral : 3.683 31.876 2562 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.48 % Allowed : 33.82 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.18), residues: 2343 helix: 2.51 (0.14), residues: 1351 sheet: -1.14 (0.37), residues: 174 loop : -0.82 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 671 HIS 0.007 0.001 HIS F 205 PHE 0.019 0.001 PHE G 141 TYR 0.011 0.001 TYR D 549 ARG 0.008 0.001 ARG B 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 296 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 GLN cc_start: 0.7777 (pp30) cc_final: 0.7142 (mt0) REVERT: H 86 ASP cc_start: 0.1875 (OUTLIER) cc_final: 0.1398 (p0) REVERT: H 192 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7228 (mtt) REVERT: H 207 GLN cc_start: 0.7885 (tp40) cc_final: 0.7522 (mt0) REVERT: F 65 ARG cc_start: 0.7236 (pmt170) cc_final: 0.6888 (pmt170) REVERT: F 78 LYS cc_start: 0.8575 (ptmt) cc_final: 0.7831 (pttm) REVERT: F 149 ASN cc_start: 0.8112 (t0) cc_final: 0.7733 (t0) REVERT: F 204 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6914 (tpm170) REVERT: F 206 LYS cc_start: 0.6854 (tmmt) cc_final: 0.6282 (mtpp) REVERT: C 463 MET cc_start: 0.7591 (mmm) cc_final: 0.6660 (mmt) REVERT: C 627 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 673 TYR cc_start: 0.7421 (t80) cc_final: 0.7213 (t80) REVERT: C 819 ARG cc_start: 0.7025 (ttp80) cc_final: 0.6592 (tpp80) REVERT: B 407 MET cc_start: 0.6589 (pmm) cc_final: 0.5350 (pmm) REVERT: B 670 MET cc_start: 0.7943 (ppp) cc_final: 0.7512 (pmt) REVERT: B 708 MET cc_start: 0.8593 (tpp) cc_final: 0.8082 (tpp) REVERT: A 767 TRP cc_start: 0.7242 (m-90) cc_final: 0.6802 (m-90) REVERT: D 496 MET cc_start: 0.8261 (ptp) cc_final: 0.7145 (mtm) REVERT: D 660 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7662 (mtm-85) REVERT: E 6 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.7951 (mmm160) REVERT: E 117 MET cc_start: 0.5077 (tpt) cc_final: 0.4846 (tpt) REVERT: E 206 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7956 (ttmm) REVERT: G 11 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8129 (tm) REVERT: G 69 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6940 (pt) REVERT: G 78 LYS cc_start: 0.7641 (ptpt) cc_final: 0.7440 (ptpt) REVERT: G 185 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7146 (mm) outliers start: 45 outliers final: 29 residues processed: 320 average time/residue: 0.9922 time to fit residues: 359.5861 Evaluate side-chains 326 residues out of total 1983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 MET Chi-restraints excluded: chain H residue 205 HIS Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 204 ARG Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 627 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 740 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 77 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 185 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 0.0000 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN A 714 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.223111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.164118 restraints weight = 62308.640| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 7.05 r_work: 0.3474 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18863 Z= 0.193 Angle : 0.665 12.381 25523 Z= 0.320 Chirality : 0.040 0.169 2883 Planarity : 0.004 0.057 3153 Dihedral : 3.691 32.055 2562 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 33.87 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2343 helix: 2.45 (0.14), residues: 1353 sheet: -1.17 (0.38), residues: 174 loop : -0.83 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 671 HIS 0.006 0.001 HIS F 205 PHE 0.029 0.001 PHE E 73 TYR 0.016 0.001 TYR G 156 ARG 0.009 0.001 ARG C 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8119.47 seconds wall clock time: 143 minutes 55.58 seconds (8635.58 seconds total)