Starting phenix.real_space_refine on Tue Feb 20 20:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8j_32357/02_2024/7w8j_32357.pdb" } resolution = 2.5 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 100 5.16 5 C 17914 2.51 5 N 4990 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C GLU 628": "OE1" <-> "OE2" Residue "C GLU 635": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E GLU 347": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "E GLU 506": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E GLU 568": "OE1" <-> "OE2" Residue "E GLU 580": "OE1" <-> "OE2" Residue "E GLU 628": "OE1" <-> "OE2" Residue "E GLU 635": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 369": "OE1" <-> "OE2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G GLU 506": "OE1" <-> "OE2" Residue "G GLU 554": "OE1" <-> "OE2" Residue "G GLU 635": "OE1" <-> "OE2" Residue "G GLU 640": "OE1" <-> "OE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28678 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6006 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6122 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "C" Number of atoms: 6014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6113 Chain: "D" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "E" Number of atoms: 6014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6113 Chain: "F" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "G" Number of atoms: 6006 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6122 Chain: "H" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 25.03, per 1000 atoms: 0.87 Number of scatterers: 28678 At special positions: 0 Unit cell: (123.05, 153.01, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 100 16.00 O 5670 8.00 N 4990 7.00 C 17914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.02 Conformation dependent library (CDL) restraints added in 8.5 seconds 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6460 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 44 sheets defined 25.8% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.566A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.118A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 623 through 631 removed outlier: 6.153A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.589A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.544A pdb=" N ARG B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.355A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.946A pdb=" N MET B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 131 Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.561A pdb=" N ARG C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.119A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 537 Processing helix chain 'C' and resid 594 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 623 through 631 removed outlier: 6.164A pdb=" N GLU C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG C 629 " --> pdb=" O GLN C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 688 through 691 Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 726 through 733 removed outlier: 3.590A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 733 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 19 through 41 removed outlier: 3.541A pdb=" N ARG D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 removed outlier: 4.354A pdb=" N GLU D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 72 removed outlier: 3.944A pdb=" N MET D 72 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 131 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.561A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 458 through 462 Processing helix chain 'E' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.118A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 600 through 605 Processing helix chain 'E' and resid 623 through 631 removed outlier: 6.164A pdb=" N GLU E 628 " --> pdb=" O SER E 625 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG E 629 " --> pdb=" O GLN E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 688 through 691 Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 726 through 733 removed outlier: 3.591A pdb=" N TRP E 729 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E 730 " --> pdb=" O ILE E 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 733 " --> pdb=" O LEU E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 739 Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 19 through 41 removed outlier: 3.541A pdb=" N ARG F 29 " --> pdb=" O PHE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 removed outlier: 4.354A pdb=" N GLU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 72 removed outlier: 3.943A pdb=" N MET F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 131 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.565A pdb=" N ARG G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 392 through 399 Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 458 through 462 Processing helix chain 'G' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS G 480 " --> pdb=" O PRO G 476 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 4.119A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 537 Processing helix chain 'G' and resid 594 through 597 Processing helix chain 'G' and resid 600 through 605 Processing helix chain 'G' and resid 623 through 631 removed outlier: 6.153A pdb=" N GLU G 628 " --> pdb=" O SER G 625 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG G 629 " --> pdb=" O GLN G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 666 Processing helix chain 'G' and resid 688 through 691 Processing helix chain 'G' and resid 716 through 718 No H-bonds generated for 'chain 'G' and resid 716 through 718' Processing helix chain 'G' and resid 726 through 733 removed outlier: 3.589A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 733 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 734 through 739 Processing helix chain 'G' and resid 740 through 754 Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 removed outlier: 3.544A pdb=" N ARG H 29 " --> pdb=" O PHE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.355A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 72 removed outlier: 3.945A pdb=" N MET H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 39 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 58 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 41 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 56 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE A 128 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 111 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE A 128 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 111 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA A 329 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 307 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.506A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N PHE A 611 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ARG A 660 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N PHE A 613 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N LEU A 658 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N HIS A 615 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR A 656 " --> pdb=" O HIS A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.506A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 611 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.513A pdb=" N ALA B 89 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 523 removed outlier: 4.405A pdb=" N GLY A 591 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL C 39 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 58 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU C 41 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU C 56 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA C 329 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 307 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB9, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.526A pdb=" N ALA D 89 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC4, first strand: chain 'C' and resid 522 through 523 removed outlier: 4.408A pdb=" N GLY C 591 " --> pdb=" O ILE C 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.585A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL E 39 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 58 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU E 41 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU E 56 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.331A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.331A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA E 329 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY E 307 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 219 through 220 Processing sheet with id=AD2, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.451A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 420 through 421 removed outlier: 6.526A pdb=" N ALA F 89 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 451 through 453 Processing sheet with id=AD6, first strand: chain 'E' and resid 522 through 523 removed outlier: 4.407A pdb=" N GLY E 591 " --> pdb=" O ILE E 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 39 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 58 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU G 41 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU G 56 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE G 128 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY G 111 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE G 128 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY G 111 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA G 329 " --> pdb=" O GLY G 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY G 307 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AE4, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.507A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N PHE G 611 " --> pdb=" O ARG G 660 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ARG G 660 " --> pdb=" O PHE G 611 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N PHE G 613 " --> pdb=" O LEU G 658 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N LEU G 658 " --> pdb=" O PHE G 613 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N HIS G 615 " --> pdb=" O TYR G 656 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR G 656 " --> pdb=" O HIS G 615 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.507A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE G 611 " --> pdb=" O THR G 685 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 420 through 421 removed outlier: 6.513A pdb=" N ALA H 89 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AE8, first strand: chain 'G' and resid 522 through 523 removed outlier: 4.404A pdb=" N GLY G 591 " --> pdb=" O ILE G 552 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3352 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: 13.99 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5546 1.33 - 1.45: 7854 1.45 - 1.58: 15646 1.58 - 1.71: 0 1.71 - 1.84: 164 Bond restraints: 29210 Sorted by residual: bond pdb=" N ARG C 264 " pdb=" CA ARG C 264 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.00e+01 bond pdb=" N ARG E 264 " pdb=" CA ARG E 264 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.00e+01 bond pdb=" N ILE G 603 " pdb=" CA ILE G 603 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.95e+01 bond pdb=" N ILE A 603 " pdb=" CA ILE A 603 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.95e+01 bond pdb=" N ARG G 264 " pdb=" CA ARG G 264 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.10e-03 1.98e+04 1.85e+01 ... (remaining 29205 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.27: 748 105.27 - 112.58: 13275 112.58 - 119.90: 13903 119.90 - 127.22: 11427 127.22 - 134.53: 361 Bond angle restraints: 39714 Sorted by residual: angle pdb=" CA ASP A 537 " pdb=" CB ASP A 537 " pdb=" CG ASP A 537 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA ASP G 537 " pdb=" CB ASP G 537 " pdb=" CG ASP G 537 " ideal model delta sigma weight residual 112.60 119.42 -6.82 1.00e+00 1.00e+00 4.66e+01 angle pdb=" C ARG C 447 " pdb=" N GLY C 448 " pdb=" CA GLY C 448 " ideal model delta sigma weight residual 120.10 124.92 -4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" C ARG E 447 " pdb=" N GLY E 448 " pdb=" CA GLY E 448 " ideal model delta sigma weight residual 120.10 124.92 -4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" C ARG C 660 " pdb=" N TYR C 661 " pdb=" CA TYR C 661 " ideal model delta sigma weight residual 120.95 128.00 -7.05 1.40e+00 5.10e-01 2.53e+01 ... (remaining 39709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15710 17.91 - 35.82: 1014 35.82 - 53.72: 192 53.72 - 71.63: 86 71.63 - 89.54: 52 Dihedral angle restraints: 17054 sinusoidal: 6838 harmonic: 10216 Sorted by residual: dihedral pdb=" CA SER C 114 " pdb=" C SER C 114 " pdb=" N ARG C 115 " pdb=" CA ARG C 115 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA SER E 114 " pdb=" C SER E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA SER A 114 " pdb=" C SER A 114 " pdb=" N ARG A 115 " pdb=" CA ARG A 115 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1361 0.042 - 0.084: 1260 0.084 - 0.126: 890 0.126 - 0.168: 411 0.168 - 0.210: 100 Chirality restraints: 4022 Sorted by residual: chirality pdb=" CA ARG E 31 " pdb=" N ARG E 31 " pdb=" C ARG E 31 " pdb=" CB ARG E 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG C 31 " pdb=" N ARG C 31 " pdb=" C ARG C 31 " pdb=" CB ARG C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 4019 not shown) Planarity restraints: 5284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 740 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" CG ASN G 740 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN G 740 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN G 740 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 740 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" CG ASN A 740 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 740 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 740 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 370 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CG ASP C 370 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASP C 370 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP C 370 " 0.021 2.00e-02 2.50e+03 ... (remaining 5281 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 18552 3.11 - 3.70: 45639 3.70 - 4.30: 71356 4.30 - 4.90: 115454 Nonbonded interactions: 251132 Sorted by model distance: nonbonded pdb=" OH TYR A 440 " pdb="FE FE A 801 " model vdw 1.909 2.260 nonbonded pdb=" OH TYR G 440 " pdb="FE FE G 801 " model vdw 1.909 2.260 nonbonded pdb=" OH TYR C 440 " pdb="FE FE C 801 " model vdw 1.911 2.260 nonbonded pdb=" OH TYR E 440 " pdb="FE FE E 801 " model vdw 1.912 2.260 nonbonded pdb=" OH TYR A 399 " pdb="FE FE A 801 " model vdw 1.914 2.260 ... (remaining 251127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'C' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'E' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'G' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 1.600 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: 8.850 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 92.590 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.180 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.014 0.057 29210 Z= 0.903 Angle : 1.616 7.046 39714 Z= 1.200 Chirality : 0.082 0.210 4022 Planarity : 0.004 0.046 5284 Dihedral : 14.207 89.538 10594 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.24 % Allowed : 4.51 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 3550 helix: -0.07 (0.18), residues: 660 sheet: 0.14 (0.20), residues: 684 loop : -0.34 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 22 HIS 0.019 0.002 HIS A 322 PHE 0.033 0.002 PHE F 53 TYR 0.037 0.003 TYR D 90 ARG 0.030 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 402 time to evaluate : 3.678 Fit side-chains REVERT: A 22 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7810 (mtm180) REVERT: A 211 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 255 GLU cc_start: 0.7409 (tp30) cc_final: 0.6880 (mm-30) REVERT: A 345 ASP cc_start: 0.7973 (m-30) cc_final: 0.7548 (m-30) REVERT: A 347 GLU cc_start: 0.7814 (pt0) cc_final: 0.7562 (pt0) REVERT: A 364 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6407 (mtm-85) REVERT: A 409 ASP cc_start: 0.6899 (m-30) cc_final: 0.6682 (m-30) REVERT: A 537 ASP cc_start: 0.7016 (p0) cc_final: 0.6743 (m-30) REVERT: A 588 ARG cc_start: 0.7433 (mmt90) cc_final: 0.6654 (mtp180) REVERT: A 627 ASP cc_start: 0.7343 (t0) cc_final: 0.6628 (t0) REVERT: A 641 GLU cc_start: 0.6341 (mt-10) cc_final: 0.6037 (mt-10) REVERT: A 659 ASP cc_start: 0.7944 (m-30) cc_final: 0.7676 (m-30) REVERT: A 717 ASN cc_start: 0.7407 (t0) cc_final: 0.6768 (t0) REVERT: A 736 ASN cc_start: 0.7962 (t0) cc_final: 0.7672 (t0) REVERT: A 745 MET cc_start: 0.8314 (ttm) cc_final: 0.7944 (ttm) REVERT: A 756 ASP cc_start: 0.7319 (m-30) cc_final: 0.6550 (p0) REVERT: A 757 GLU cc_start: 0.7295 (tt0) cc_final: 0.6984 (tt0) REVERT: B 11 ASP cc_start: 0.7169 (t0) cc_final: 0.6545 (t70) REVERT: B 28 GLU cc_start: 0.6688 (tp30) cc_final: 0.6442 (tp30) REVERT: B 62 TYR cc_start: 0.7517 (m-80) cc_final: 0.7132 (m-80) REVERT: B 90 TYR cc_start: 0.8302 (m-80) cc_final: 0.7591 (m-80) REVERT: B 110 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7762 (mptm) REVERT: C 31 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7528 (ttp-170) REVERT: C 63 GLU cc_start: 0.7606 (tt0) cc_final: 0.7350 (tt0) REVERT: C 130 ASP cc_start: 0.6212 (t70) cc_final: 0.5895 (t70) REVERT: C 225 GLN cc_start: 0.6846 (mt0) cc_final: 0.5832 (pp30) REVERT: C 264 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7155 (mtp180) REVERT: C 299 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6042 (tpt170) REVERT: C 343 GLU cc_start: 0.7160 (tt0) cc_final: 0.6779 (mm-30) REVERT: C 506 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6545 (mp0) REVERT: C 628 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6652 (tp30) REVERT: C 737 ASP cc_start: 0.7141 (t0) cc_final: 0.6695 (t70) REVERT: C 757 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 11 ASP cc_start: 0.7786 (t0) cc_final: 0.7136 (t0) REVERT: D 14 ASN cc_start: 0.7776 (m-40) cc_final: 0.7475 (m-40) REVERT: D 28 GLU cc_start: 0.6655 (tt0) cc_final: 0.6438 (tp30) REVERT: D 36 ASP cc_start: 0.6830 (m-30) cc_final: 0.6490 (m-30) REVERT: D 78 ARG cc_start: 0.8392 (ptm160) cc_final: 0.8161 (ttm-80) REVERT: E 31 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7443 (ttp-170) REVERT: E 63 GLU cc_start: 0.7608 (tt0) cc_final: 0.7354 (tt0) REVERT: E 130 ASP cc_start: 0.6205 (t70) cc_final: 0.5915 (t70) REVERT: E 211 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 225 GLN cc_start: 0.6846 (mt0) cc_final: 0.5832 (pp30) REVERT: E 264 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7157 (mtp180) REVERT: E 299 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6039 (tpt170) REVERT: E 343 GLU cc_start: 0.7168 (tt0) cc_final: 0.6783 (mm-30) REVERT: E 506 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6547 (mp0) REVERT: E 628 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6651 (tp30) REVERT: E 737 ASP cc_start: 0.7143 (t0) cc_final: 0.6696 (t70) REVERT: E 757 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6864 (mt-10) REVERT: F 11 ASP cc_start: 0.7806 (t0) cc_final: 0.7131 (t0) REVERT: F 14 ASN cc_start: 0.7777 (m-40) cc_final: 0.7436 (m-40) REVERT: F 28 GLU cc_start: 0.6651 (tt0) cc_final: 0.6435 (tp30) REVERT: F 36 ASP cc_start: 0.6829 (m-30) cc_final: 0.6489 (m-30) REVERT: F 78 ARG cc_start: 0.8388 (ptm160) cc_final: 0.8162 (ttm-80) REVERT: G 22 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7809 (mtm180) REVERT: G 211 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7201 (mt-10) REVERT: G 255 GLU cc_start: 0.7426 (tp30) cc_final: 0.6892 (mm-30) REVERT: G 345 ASP cc_start: 0.7966 (m-30) cc_final: 0.7546 (m-30) REVERT: G 347 GLU cc_start: 0.7818 (pt0) cc_final: 0.7565 (pt0) REVERT: G 364 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: G 409 ASP cc_start: 0.6907 (m-30) cc_final: 0.6688 (m-30) REVERT: G 537 ASP cc_start: 0.7020 (p0) cc_final: 0.6742 (m-30) REVERT: G 588 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6671 (mtp180) REVERT: G 627 ASP cc_start: 0.7345 (t0) cc_final: 0.6632 (t0) REVERT: G 641 GLU cc_start: 0.6334 (mt-10) cc_final: 0.6034 (mt-10) REVERT: G 659 ASP cc_start: 0.7944 (m-30) cc_final: 0.7677 (m-30) REVERT: G 717 ASN cc_start: 0.7407 (t0) cc_final: 0.6769 (t0) REVERT: G 736 ASN cc_start: 0.7963 (t0) cc_final: 0.7673 (t0) REVERT: G 745 MET cc_start: 0.8316 (ttm) cc_final: 0.7947 (ttm) REVERT: G 756 ASP cc_start: 0.7318 (m-30) cc_final: 0.6551 (p0) REVERT: G 757 GLU cc_start: 0.7296 (tt0) cc_final: 0.6986 (tt0) REVERT: H 11 ASP cc_start: 0.7172 (t0) cc_final: 0.6548 (t70) REVERT: H 28 GLU cc_start: 0.6692 (tp30) cc_final: 0.6440 (tp30) REVERT: H 62 TYR cc_start: 0.7517 (m-80) cc_final: 0.7134 (m-80) REVERT: H 90 TYR cc_start: 0.8301 (m-80) cc_final: 0.7591 (m-80) REVERT: H 110 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7762 (mptm) outliers start: 4 outliers final: 0 residues processed: 406 average time/residue: 1.7912 time to fit residues: 824.7027 Evaluate side-chains 302 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 3.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 626 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29210 Z= 0.199 Angle : 0.566 7.793 39714 Z= 0.309 Chirality : 0.046 0.188 4022 Planarity : 0.004 0.034 5284 Dihedral : 4.598 25.309 4010 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.26 % Allowed : 6.86 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3550 helix: 1.80 (0.20), residues: 680 sheet: 0.31 (0.19), residues: 756 loop : -0.02 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 22 HIS 0.005 0.001 HIS E 465 PHE 0.017 0.002 PHE H 120 TYR 0.029 0.002 TYR A 661 ARG 0.004 0.001 ARG E 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 3.215 Fit side-chains REVERT: A 211 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 343 GLU cc_start: 0.7131 (tp30) cc_final: 0.6873 (tm-30) REVERT: A 347 GLU cc_start: 0.8091 (pt0) cc_final: 0.7790 (pt0) REVERT: A 409 ASP cc_start: 0.6891 (m-30) cc_final: 0.6626 (m-30) REVERT: A 425 ASP cc_start: 0.7014 (m-30) cc_final: 0.6714 (m-30) REVERT: A 491 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: A 641 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6306 (mt-10) REVERT: A 659 ASP cc_start: 0.7911 (m-30) cc_final: 0.7570 (m-30) REVERT: A 717 ASN cc_start: 0.7237 (t0) cc_final: 0.6361 (t0) REVERT: A 736 ASN cc_start: 0.7710 (t0) cc_final: 0.7363 (t0) REVERT: A 745 MET cc_start: 0.8332 (ttm) cc_final: 0.8021 (ttm) REVERT: B 62 TYR cc_start: 0.7495 (m-80) cc_final: 0.7028 (m-80) REVERT: B 90 TYR cc_start: 0.8295 (m-80) cc_final: 0.7614 (m-80) REVERT: B 110 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7474 (mptm) REVERT: C 1 MET cc_start: 0.6654 (ptp) cc_final: 0.6382 (ptt) REVERT: C 168 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6854 (tp30) REVERT: C 299 ARG cc_start: 0.6922 (mtp85) cc_final: 0.5905 (tpt170) REVERT: C 343 GLU cc_start: 0.7218 (tt0) cc_final: 0.6878 (mm-30) REVERT: C 506 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6507 (mp0) REVERT: C 628 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6673 (tp30) REVERT: C 737 ASP cc_start: 0.7563 (t0) cc_final: 0.7089 (t70) REVERT: D 28 GLU cc_start: 0.6940 (tt0) cc_final: 0.6715 (tt0) REVERT: D 51 ASN cc_start: 0.7138 (t0) cc_final: 0.6737 (t0) REVERT: E 1 MET cc_start: 0.6655 (ptp) cc_final: 0.6383 (ptt) REVERT: E 168 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6875 (tp30) REVERT: E 211 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7750 (mt-10) REVERT: E 299 ARG cc_start: 0.6921 (mtp85) cc_final: 0.5902 (tpt170) REVERT: E 343 GLU cc_start: 0.7221 (tt0) cc_final: 0.6880 (mm-30) REVERT: E 506 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6476 (mp0) REVERT: E 628 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6673 (tp30) REVERT: E 737 ASP cc_start: 0.7563 (t0) cc_final: 0.7089 (t70) REVERT: F 28 GLU cc_start: 0.6939 (tt0) cc_final: 0.6712 (tt0) REVERT: F 51 ASN cc_start: 0.7097 (t0) cc_final: 0.6694 (t0) REVERT: G 211 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7344 (mt-10) REVERT: G 343 GLU cc_start: 0.7126 (tp30) cc_final: 0.6868 (tm-30) REVERT: G 347 GLU cc_start: 0.8092 (pt0) cc_final: 0.7790 (pt0) REVERT: G 409 ASP cc_start: 0.6906 (m-30) cc_final: 0.6641 (m-30) REVERT: G 425 ASP cc_start: 0.7013 (m-30) cc_final: 0.6713 (m-30) REVERT: G 491 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: G 659 ASP cc_start: 0.7911 (m-30) cc_final: 0.7569 (m-30) REVERT: G 717 ASN cc_start: 0.7234 (t0) cc_final: 0.6359 (t0) REVERT: G 736 ASN cc_start: 0.7710 (t0) cc_final: 0.7362 (t0) REVERT: G 745 MET cc_start: 0.8333 (ttm) cc_final: 0.8023 (ttm) REVERT: H 62 TYR cc_start: 0.7493 (m-80) cc_final: 0.7029 (m-80) REVERT: H 90 TYR cc_start: 0.8294 (m-80) cc_final: 0.7618 (m-80) REVERT: H 110 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7480 (mptm) outliers start: 33 outliers final: 16 residues processed: 345 average time/residue: 1.6829 time to fit residues: 664.6169 Evaluate side-chains 320 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 302 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 83 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 chunk 345 optimal weight: 0.0370 chunk 285 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29210 Z= 0.362 Angle : 0.650 8.116 39714 Z= 0.354 Chirality : 0.050 0.193 4022 Planarity : 0.006 0.051 5284 Dihedral : 5.005 24.928 4010 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.10 % Allowed : 8.21 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3550 helix: 1.64 (0.20), residues: 680 sheet: 0.34 (0.20), residues: 732 loop : -0.14 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 22 HIS 0.007 0.002 HIS C 97 PHE 0.019 0.003 PHE A 187 TYR 0.033 0.002 TYR G 661 ARG 0.007 0.001 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 299 time to evaluate : 3.122 Fit side-chains REVERT: A 343 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: A 347 GLU cc_start: 0.8194 (pt0) cc_final: 0.7920 (pt0) REVERT: A 409 ASP cc_start: 0.6916 (m-30) cc_final: 0.6710 (m-30) REVERT: A 491 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: A 659 ASP cc_start: 0.7996 (m-30) cc_final: 0.7572 (m-30) REVERT: A 717 ASN cc_start: 0.7466 (t0) cc_final: 0.7105 (t0) REVERT: A 736 ASN cc_start: 0.7764 (t0) cc_final: 0.7423 (t0) REVERT: A 745 MET cc_start: 0.8300 (ttm) cc_final: 0.7822 (ttp) REVERT: B 62 TYR cc_start: 0.7571 (m-80) cc_final: 0.7170 (m-80) REVERT: B 83 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8107 (t) REVERT: B 90 TYR cc_start: 0.8245 (m-80) cc_final: 0.7376 (m-80) REVERT: B 110 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7255 (mmtm) REVERT: B 116 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: C 59 LYS cc_start: 0.8140 (pttm) cc_final: 0.7894 (tptp) REVERT: C 211 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: C 294 TYR cc_start: 0.6771 (m-80) cc_final: 0.6530 (m-80) REVERT: C 299 ARG cc_start: 0.6870 (mtp85) cc_final: 0.5976 (tpt170) REVERT: C 506 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6471 (mp0) REVERT: C 608 MET cc_start: 0.8176 (tpt) cc_final: 0.7898 (tpt) REVERT: C 628 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6598 (tp30) REVERT: C 737 ASP cc_start: 0.7603 (t0) cc_final: 0.7186 (t70) REVERT: D 28 GLU cc_start: 0.7036 (tt0) cc_final: 0.6734 (tt0) REVERT: D 32 LYS cc_start: 0.7510 (mttm) cc_final: 0.7137 (mttm) REVERT: D 88 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7183 (t70) REVERT: E 59 LYS cc_start: 0.8141 (pttm) cc_final: 0.7896 (tptp) REVERT: E 211 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7447 (mt-10) REVERT: E 294 TYR cc_start: 0.6773 (m-80) cc_final: 0.6534 (m-80) REVERT: E 299 ARG cc_start: 0.6869 (mtp85) cc_final: 0.5974 (tpt170) REVERT: E 506 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6497 (mp0) REVERT: E 608 MET cc_start: 0.8175 (tpt) cc_final: 0.7896 (tpt) REVERT: E 628 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6596 (tp30) REVERT: E 737 ASP cc_start: 0.7604 (t0) cc_final: 0.7185 (t70) REVERT: F 28 GLU cc_start: 0.7036 (tt0) cc_final: 0.6734 (tt0) REVERT: F 32 LYS cc_start: 0.7508 (mttm) cc_final: 0.7151 (mttm) REVERT: F 88 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7132 (t70) REVERT: G 343 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: G 347 GLU cc_start: 0.8195 (pt0) cc_final: 0.7918 (pt0) REVERT: G 409 ASP cc_start: 0.6922 (m-30) cc_final: 0.6716 (m-30) REVERT: G 491 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: G 659 ASP cc_start: 0.7998 (m-30) cc_final: 0.7573 (m-30) REVERT: G 717 ASN cc_start: 0.7466 (t0) cc_final: 0.7105 (t0) REVERT: G 736 ASN cc_start: 0.7766 (t0) cc_final: 0.7425 (t0) REVERT: G 745 MET cc_start: 0.8300 (ttm) cc_final: 0.7822 (ttp) REVERT: H 62 TYR cc_start: 0.7570 (m-80) cc_final: 0.7171 (m-80) REVERT: H 83 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8108 (t) REVERT: H 90 TYR cc_start: 0.8245 (m-80) cc_final: 0.7369 (m-80) REVERT: H 110 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7252 (mmtm) REVERT: H 116 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6981 (mtt) outliers start: 58 outliers final: 20 residues processed: 328 average time/residue: 1.6789 time to fit residues: 631.5675 Evaluate side-chains 320 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 289 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 321 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29210 Z= 0.211 Angle : 0.549 7.936 39714 Z= 0.297 Chirality : 0.046 0.176 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.690 24.620 4010 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.90 % Allowed : 8.89 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3550 helix: 1.94 (0.20), residues: 656 sheet: 0.36 (0.20), residues: 728 loop : -0.10 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 473 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.002 PHE E 713 TYR 0.027 0.002 TYR A 661 ARG 0.005 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: A 347 GLU cc_start: 0.8134 (pt0) cc_final: 0.7854 (pt0) REVERT: A 409 ASP cc_start: 0.6757 (m-30) cc_final: 0.6447 (m-30) REVERT: A 425 ASP cc_start: 0.6981 (m-30) cc_final: 0.6654 (m-30) REVERT: A 491 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: A 506 GLU cc_start: 0.7403 (tt0) cc_final: 0.6407 (tp30) REVERT: A 659 ASP cc_start: 0.7970 (m-30) cc_final: 0.7561 (m-30) REVERT: A 717 ASN cc_start: 0.7434 (t0) cc_final: 0.6524 (t0) REVERT: A 736 ASN cc_start: 0.7707 (t0) cc_final: 0.7379 (t0) REVERT: A 745 MET cc_start: 0.8278 (ttm) cc_final: 0.7788 (ttp) REVERT: B 62 TYR cc_start: 0.7408 (m-80) cc_final: 0.6977 (m-80) REVERT: B 90 TYR cc_start: 0.8331 (m-80) cc_final: 0.7378 (m-80) REVERT: B 110 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7245 (mmtm) REVERT: C 29 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: C 59 LYS cc_start: 0.8122 (pttm) cc_final: 0.7764 (tptp) REVERT: C 168 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6960 (tm-30) REVERT: C 211 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7676 (mt-10) REVERT: C 264 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6647 (mtt180) REVERT: C 294 TYR cc_start: 0.6767 (m-80) cc_final: 0.6517 (m-80) REVERT: C 299 ARG cc_start: 0.6898 (mtp85) cc_final: 0.5970 (tpt170) REVERT: C 506 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6510 (mp0) REVERT: C 737 ASP cc_start: 0.7598 (t0) cc_final: 0.7187 (t70) REVERT: D 28 GLU cc_start: 0.7094 (tt0) cc_final: 0.6786 (tt0) REVERT: D 32 LYS cc_start: 0.7516 (mttm) cc_final: 0.7118 (mttm) REVERT: D 88 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7028 (t70) REVERT: D 130 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6522 (tp30) REVERT: E 29 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: E 59 LYS cc_start: 0.8121 (pttm) cc_final: 0.7765 (tptp) REVERT: E 264 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6651 (mtt180) REVERT: E 294 TYR cc_start: 0.6769 (m-80) cc_final: 0.6521 (m-80) REVERT: E 299 ARG cc_start: 0.6897 (mtp85) cc_final: 0.5968 (tpt170) REVERT: E 506 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6498 (mp0) REVERT: E 737 ASP cc_start: 0.7600 (t0) cc_final: 0.7187 (t70) REVERT: F 28 GLU cc_start: 0.7091 (tt0) cc_final: 0.6785 (tt0) REVERT: F 32 LYS cc_start: 0.7502 (mttm) cc_final: 0.7108 (mttm) REVERT: F 130 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6524 (tp30) REVERT: G 343 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: G 347 GLU cc_start: 0.8134 (pt0) cc_final: 0.7853 (pt0) REVERT: G 409 ASP cc_start: 0.6761 (m-30) cc_final: 0.6454 (m-30) REVERT: G 425 ASP cc_start: 0.6983 (m-30) cc_final: 0.6655 (m-30) REVERT: G 491 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: G 506 GLU cc_start: 0.7402 (tt0) cc_final: 0.6406 (tp30) REVERT: G 659 ASP cc_start: 0.7974 (m-30) cc_final: 0.7564 (m-30) REVERT: G 717 ASN cc_start: 0.7434 (t0) cc_final: 0.6524 (t0) REVERT: G 736 ASN cc_start: 0.7706 (t0) cc_final: 0.7380 (t0) REVERT: G 745 MET cc_start: 0.8278 (ttm) cc_final: 0.7788 (ttp) REVERT: H 62 TYR cc_start: 0.7406 (m-80) cc_final: 0.6976 (m-80) REVERT: H 90 TYR cc_start: 0.8332 (m-80) cc_final: 0.7378 (m-80) REVERT: H 110 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7244 (mmtm) outliers start: 50 outliers final: 24 residues processed: 325 average time/residue: 1.5950 time to fit residues: 596.1272 Evaluate side-chains 326 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 293 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29210 Z= 0.354 Angle : 0.638 7.775 39714 Z= 0.346 Chirality : 0.050 0.188 4022 Planarity : 0.005 0.053 5284 Dihedral : 4.988 24.674 4010 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.41 % Allowed : 8.66 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3550 helix: 1.69 (0.19), residues: 656 sheet: 0.48 (0.20), residues: 708 loop : -0.19 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 473 HIS 0.006 0.002 HIS C 97 PHE 0.018 0.003 PHE A 187 TYR 0.029 0.002 TYR G 661 ARG 0.005 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 292 time to evaluate : 3.526 Fit side-chains REVERT: A 343 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6843 (tm-30) REVERT: A 347 GLU cc_start: 0.8189 (pt0) cc_final: 0.7898 (pt0) REVERT: A 409 ASP cc_start: 0.6736 (m-30) cc_final: 0.6435 (m-30) REVERT: A 491 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7002 (mm-30) REVERT: A 506 GLU cc_start: 0.7431 (tt0) cc_final: 0.6406 (tp30) REVERT: A 635 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: A 659 ASP cc_start: 0.8003 (m-30) cc_final: 0.7571 (m-30) REVERT: A 717 ASN cc_start: 0.7511 (t0) cc_final: 0.7106 (t0) REVERT: A 736 ASN cc_start: 0.7730 (t0) cc_final: 0.7377 (t0) REVERT: A 745 MET cc_start: 0.8284 (ttm) cc_final: 0.7820 (ttp) REVERT: B 62 TYR cc_start: 0.7501 (m-80) cc_final: 0.6999 (m-80) REVERT: B 90 TYR cc_start: 0.8356 (m-80) cc_final: 0.7321 (m-80) REVERT: B 110 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7217 (mmtm) REVERT: B 116 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7001 (mtt) REVERT: C 29 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: C 59 LYS cc_start: 0.8171 (pttm) cc_final: 0.7809 (tptp) REVERT: C 130 ASP cc_start: 0.6479 (t70) cc_final: 0.6235 (t70) REVERT: C 211 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: C 264 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6809 (mtt180) REVERT: C 294 TYR cc_start: 0.6779 (m-80) cc_final: 0.6574 (m-10) REVERT: C 299 ARG cc_start: 0.6863 (mtp85) cc_final: 0.5989 (tpt170) REVERT: C 506 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6469 (mp0) REVERT: C 608 MET cc_start: 0.8164 (tpt) cc_final: 0.7907 (tpt) REVERT: D 28 GLU cc_start: 0.6879 (tt0) cc_final: 0.6657 (tt0) REVERT: D 88 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7172 (t70) REVERT: D 130 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6621 (tp30) REVERT: E 29 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: E 59 LYS cc_start: 0.8168 (pttm) cc_final: 0.7809 (tptp) REVERT: E 130 ASP cc_start: 0.6479 (t70) cc_final: 0.6215 (t70) REVERT: E 168 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6955 (tm-30) REVERT: E 264 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6813 (mtt180) REVERT: E 294 TYR cc_start: 0.6782 (m-80) cc_final: 0.6576 (m-10) REVERT: E 299 ARG cc_start: 0.6858 (mtp85) cc_final: 0.5985 (tpt170) REVERT: E 506 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6467 (mp0) REVERT: E 608 MET cc_start: 0.8163 (tpt) cc_final: 0.7907 (tpt) REVERT: F 28 GLU cc_start: 0.6875 (tt0) cc_final: 0.6654 (tt0) REVERT: F 88 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7177 (t70) REVERT: F 130 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6622 (tp30) REVERT: G 343 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: G 347 GLU cc_start: 0.8191 (pt0) cc_final: 0.7896 (pt0) REVERT: G 409 ASP cc_start: 0.6740 (m-30) cc_final: 0.6441 (m-30) REVERT: G 491 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: G 506 GLU cc_start: 0.7430 (tt0) cc_final: 0.6407 (tp30) REVERT: G 635 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: G 659 ASP cc_start: 0.8005 (m-30) cc_final: 0.7574 (m-30) REVERT: G 717 ASN cc_start: 0.7520 (t0) cc_final: 0.7111 (t0) REVERT: G 736 ASN cc_start: 0.7732 (t0) cc_final: 0.7379 (t0) REVERT: G 745 MET cc_start: 0.8285 (ttm) cc_final: 0.7821 (ttp) REVERT: H 62 TYR cc_start: 0.7501 (m-80) cc_final: 0.7000 (m-80) REVERT: H 90 TYR cc_start: 0.8352 (m-80) cc_final: 0.7321 (m-80) REVERT: H 110 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7218 (mmtm) REVERT: H 116 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7000 (mtt) outliers start: 65 outliers final: 31 residues processed: 320 average time/residue: 1.6828 time to fit residues: 617.7984 Evaluate side-chains 334 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 288 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 635 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 chunk 282 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29210 Z= 0.270 Angle : 0.586 8.125 39714 Z= 0.317 Chirality : 0.047 0.178 4022 Planarity : 0.005 0.040 5284 Dihedral : 4.855 24.412 4010 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.44 % Allowed : 8.69 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3550 helix: 1.76 (0.20), residues: 656 sheet: 0.48 (0.20), residues: 708 loop : -0.19 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 473 HIS 0.005 0.001 HIS E 97 PHE 0.015 0.002 PHE A 187 TYR 0.029 0.002 TYR A 661 ARG 0.004 0.001 ARG G 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 304 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6872 (tm-30) REVERT: A 347 GLU cc_start: 0.8151 (pt0) cc_final: 0.7858 (pt0) REVERT: A 409 ASP cc_start: 0.6723 (m-30) cc_final: 0.6413 (m-30) REVERT: A 447 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6945 (tmm-80) REVERT: A 491 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: A 506 GLU cc_start: 0.7427 (tt0) cc_final: 0.6403 (tp30) REVERT: A 659 ASP cc_start: 0.7986 (m-30) cc_final: 0.7560 (m-30) REVERT: A 717 ASN cc_start: 0.7509 (t0) cc_final: 0.6580 (t0) REVERT: A 736 ASN cc_start: 0.7697 (t0) cc_final: 0.7372 (t0) REVERT: B 62 TYR cc_start: 0.7476 (m-80) cc_final: 0.6996 (m-80) REVERT: B 90 TYR cc_start: 0.8372 (m-80) cc_final: 0.7291 (m-80) REVERT: B 110 LYS cc_start: 0.7780 (mmmt) cc_final: 0.7173 (mmtm) REVERT: B 116 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: C 29 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: C 59 LYS cc_start: 0.8122 (pttm) cc_final: 0.7701 (tptp) REVERT: C 211 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: C 264 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6775 (mtt180) REVERT: C 299 ARG cc_start: 0.6885 (mtp85) cc_final: 0.5967 (tpt170) REVERT: C 506 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6465 (mp0) REVERT: C 608 MET cc_start: 0.8163 (tpt) cc_final: 0.7912 (tpt) REVERT: D 28 GLU cc_start: 0.6930 (tt0) cc_final: 0.6705 (tt0) REVERT: D 88 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7076 (t70) REVERT: E 29 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: E 59 LYS cc_start: 0.8122 (pttm) cc_final: 0.7701 (tptp) REVERT: E 168 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6978 (tm-30) REVERT: E 264 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6780 (mtt180) REVERT: E 299 ARG cc_start: 0.6883 (mtp85) cc_final: 0.5964 (tpt170) REVERT: E 506 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6460 (mp0) REVERT: E 608 MET cc_start: 0.8160 (tpt) cc_final: 0.7908 (tpt) REVERT: F 28 GLU cc_start: 0.6925 (tt0) cc_final: 0.6702 (tt0) REVERT: F 88 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7077 (t70) REVERT: G 343 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: G 347 GLU cc_start: 0.8147 (pt0) cc_final: 0.7854 (pt0) REVERT: G 409 ASP cc_start: 0.6724 (m-30) cc_final: 0.6417 (m-30) REVERT: G 447 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6945 (tmm-80) REVERT: G 491 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: G 506 GLU cc_start: 0.7428 (tt0) cc_final: 0.6405 (tp30) REVERT: G 659 ASP cc_start: 0.7994 (m-30) cc_final: 0.7566 (m-30) REVERT: G 717 ASN cc_start: 0.7507 (t0) cc_final: 0.6578 (t0) REVERT: G 736 ASN cc_start: 0.7699 (t0) cc_final: 0.7373 (t0) REVERT: H 62 TYR cc_start: 0.7477 (m-80) cc_final: 0.6996 (m-80) REVERT: H 90 TYR cc_start: 0.8371 (m-80) cc_final: 0.7293 (m-80) REVERT: H 110 LYS cc_start: 0.7781 (mmmt) cc_final: 0.7173 (mmtm) REVERT: H 116 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.6968 (mtt) outliers start: 65 outliers final: 33 residues processed: 338 average time/residue: 1.6885 time to fit residues: 661.3385 Evaluate side-chains 339 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 264 ARG Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 194 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 286 optimal weight: 0.0170 chunk 190 optimal weight: 8.9990 chunk 339 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN C 125 ASN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN E 125 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29210 Z= 0.130 Angle : 0.488 7.421 39714 Z= 0.262 Chirality : 0.043 0.173 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.346 23.576 4010 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 10.62 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3550 helix: 2.03 (0.20), residues: 656 sheet: 0.51 (0.20), residues: 716 loop : -0.02 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 525 HIS 0.003 0.001 HIS E 97 PHE 0.014 0.002 PHE D 120 TYR 0.020 0.001 TYR C 661 ARG 0.006 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 3.247 Fit side-chains REVERT: A 299 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6936 (ttp80) REVERT: A 343 GLU cc_start: 0.7177 (tp30) cc_final: 0.6967 (tm-30) REVERT: A 347 GLU cc_start: 0.8145 (pt0) cc_final: 0.7778 (pt0) REVERT: A 425 ASP cc_start: 0.7044 (m-30) cc_final: 0.6680 (m-30) REVERT: A 491 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: A 506 GLU cc_start: 0.7322 (tt0) cc_final: 0.6405 (tp30) REVERT: A 512 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7423 (mttm) REVERT: A 659 ASP cc_start: 0.7708 (m-30) cc_final: 0.7381 (m-30) REVERT: A 717 ASN cc_start: 0.7485 (t0) cc_final: 0.6547 (t0) REVERT: A 736 ASN cc_start: 0.7638 (t0) cc_final: 0.7291 (t0) REVERT: B 21 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: B 62 TYR cc_start: 0.7370 (m-80) cc_final: 0.6901 (m-80) REVERT: B 90 TYR cc_start: 0.8340 (m-80) cc_final: 0.7294 (m-80) REVERT: B 110 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7236 (mmtm) REVERT: C 29 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: C 31 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7224 (ttm110) REVERT: C 59 LYS cc_start: 0.8062 (pttm) cc_final: 0.7653 (tptp) REVERT: C 129 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6518 (mm-30) REVERT: C 299 ARG cc_start: 0.6917 (mtp85) cc_final: 0.5995 (tpt170) REVERT: C 486 ASN cc_start: 0.7870 (m-40) cc_final: 0.7266 (m110) REVERT: C 506 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6438 (mp0) REVERT: D 27 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: D 28 GLU cc_start: 0.7084 (tt0) cc_final: 0.6767 (tt0) REVERT: D 32 LYS cc_start: 0.7506 (mttm) cc_final: 0.7201 (mttm) REVERT: D 60 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7370 (p) REVERT: D 112 GLU cc_start: 0.6613 (pt0) cc_final: 0.6372 (pt0) REVERT: E 29 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: E 31 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7196 (ttm110) REVERT: E 59 LYS cc_start: 0.8060 (pttm) cc_final: 0.7652 (tptp) REVERT: E 129 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6519 (mm-30) REVERT: E 299 ARG cc_start: 0.6913 (mtp85) cc_final: 0.5991 (tpt170) REVERT: E 486 ASN cc_start: 0.7872 (m-40) cc_final: 0.7268 (m110) REVERT: E 506 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6434 (mp0) REVERT: F 27 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7200 (m-30) REVERT: F 28 GLU cc_start: 0.7079 (tt0) cc_final: 0.6763 (tt0) REVERT: F 32 LYS cc_start: 0.7495 (mttm) cc_final: 0.7213 (mttm) REVERT: F 60 SER cc_start: 0.7881 (OUTLIER) cc_final: 0.7375 (p) REVERT: G 299 ARG cc_start: 0.7237 (ttp-170) cc_final: 0.6936 (ttp80) REVERT: G 343 GLU cc_start: 0.7173 (tp30) cc_final: 0.6951 (tm-30) REVERT: G 347 GLU cc_start: 0.8140 (pt0) cc_final: 0.7774 (pt0) REVERT: G 425 ASP cc_start: 0.7044 (m-30) cc_final: 0.6678 (m-30) REVERT: G 491 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: G 506 GLU cc_start: 0.7323 (tt0) cc_final: 0.6407 (tp30) REVERT: G 512 LYS cc_start: 0.7725 (mmtp) cc_final: 0.7426 (mttm) REVERT: G 659 ASP cc_start: 0.7713 (m-30) cc_final: 0.7386 (m-30) REVERT: G 717 ASN cc_start: 0.7484 (t0) cc_final: 0.6547 (t0) REVERT: G 736 ASN cc_start: 0.7638 (t0) cc_final: 0.7290 (t0) REVERT: H 62 TYR cc_start: 0.7371 (m-80) cc_final: 0.6900 (m-80) REVERT: H 110 LYS cc_start: 0.7796 (mmmt) cc_final: 0.7564 (mmtm) outliers start: 32 outliers final: 16 residues processed: 328 average time/residue: 1.6480 time to fit residues: 621.7534 Evaluate side-chains 323 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29210 Z= 0.257 Angle : 0.573 7.892 39714 Z= 0.309 Chirality : 0.047 0.177 4022 Planarity : 0.005 0.040 5284 Dihedral : 4.673 23.771 4010 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.60 % Allowed : 10.52 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3550 helix: 1.98 (0.20), residues: 656 sheet: 0.46 (0.20), residues: 716 loop : -0.07 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 473 HIS 0.005 0.001 HIS E 97 PHE 0.017 0.002 PHE A 187 TYR 0.028 0.002 TYR G 661 ARG 0.003 0.000 ARG G 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 299 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6863 (ttp80) REVERT: A 343 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: A 347 GLU cc_start: 0.8155 (pt0) cc_final: 0.7802 (pt0) REVERT: A 425 ASP cc_start: 0.7011 (m-30) cc_final: 0.6658 (m-30) REVERT: A 447 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6915 (tmm-80) REVERT: A 491 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: A 506 GLU cc_start: 0.7313 (tt0) cc_final: 0.6400 (tp30) REVERT: A 512 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7542 (mttm) REVERT: A 659 ASP cc_start: 0.7991 (m-30) cc_final: 0.7571 (m-30) REVERT: A 717 ASN cc_start: 0.7510 (t0) cc_final: 0.6586 (t0) REVERT: A 736 ASN cc_start: 0.7677 (t0) cc_final: 0.7333 (t0) REVERT: B 62 TYR cc_start: 0.7441 (m-80) cc_final: 0.7000 (m-80) REVERT: B 90 TYR cc_start: 0.8365 (m-80) cc_final: 0.7328 (m-80) REVERT: B 110 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7168 (mmtm) REVERT: B 130 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6188 (tm-30) REVERT: C 29 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: C 59 LYS cc_start: 0.8108 (pttm) cc_final: 0.7718 (tptp) REVERT: C 299 ARG cc_start: 0.6885 (mtp85) cc_final: 0.5962 (tpt170) REVERT: C 506 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6449 (mp0) REVERT: D 28 GLU cc_start: 0.6929 (tt0) cc_final: 0.6705 (tt0) REVERT: D 130 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6661 (tp30) REVERT: E 29 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: E 59 LYS cc_start: 0.8108 (pttm) cc_final: 0.7719 (tptp) REVERT: E 168 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6970 (tm-30) REVERT: E 299 ARG cc_start: 0.6883 (mtp85) cc_final: 0.5960 (tpt170) REVERT: E 506 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6445 (mp0) REVERT: F 28 GLU cc_start: 0.6925 (tt0) cc_final: 0.6700 (tt0) REVERT: F 130 GLU cc_start: 0.6934 (tm-30) cc_final: 0.6663 (tp30) REVERT: G 299 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6864 (ttp80) REVERT: G 343 GLU cc_start: 0.7165 (tp30) cc_final: 0.6937 (tm-30) REVERT: G 347 GLU cc_start: 0.8150 (pt0) cc_final: 0.7804 (pt0) REVERT: G 425 ASP cc_start: 0.7011 (m-30) cc_final: 0.6658 (m-30) REVERT: G 447 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6916 (tmm-80) REVERT: G 491 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: G 506 GLU cc_start: 0.7309 (tt0) cc_final: 0.6398 (tp30) REVERT: G 512 LYS cc_start: 0.7820 (mmtp) cc_final: 0.7542 (mttm) REVERT: G 659 ASP cc_start: 0.7993 (m-30) cc_final: 0.7574 (m-30) REVERT: G 717 ASN cc_start: 0.7509 (t0) cc_final: 0.6586 (t0) REVERT: G 736 ASN cc_start: 0.7677 (t0) cc_final: 0.7333 (t0) REVERT: H 62 TYR cc_start: 0.7409 (m-80) cc_final: 0.6973 (m-80) REVERT: H 90 TYR cc_start: 0.8414 (m-80) cc_final: 0.7363 (m-80) REVERT: H 110 LYS cc_start: 0.7783 (mmmt) cc_final: 0.7169 (mmtm) REVERT: H 130 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6197 (tm-30) outliers start: 39 outliers final: 25 residues processed: 321 average time/residue: 1.7329 time to fit residues: 637.4532 Evaluate side-chains 330 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 298 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 296 optimal weight: 0.0570 chunk 316 optimal weight: 0.6980 chunk 324 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29210 Z= 0.222 Angle : 0.553 7.938 39714 Z= 0.298 Chirality : 0.046 0.173 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.639 23.782 4010 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 10.45 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3550 helix: 1.99 (0.20), residues: 656 sheet: 0.54 (0.20), residues: 708 loop : -0.09 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 473 HIS 0.005 0.001 HIS E 97 PHE 0.014 0.002 PHE A 187 TYR 0.027 0.002 TYR A 661 ARG 0.004 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6860 (ttp80) REVERT: A 343 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: A 347 GLU cc_start: 0.8151 (pt0) cc_final: 0.7800 (pt0) REVERT: A 425 ASP cc_start: 0.7006 (m-30) cc_final: 0.6626 (m-30) REVERT: A 447 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6899 (tmm-80) REVERT: A 491 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: A 506 GLU cc_start: 0.7304 (tt0) cc_final: 0.6392 (tp30) REVERT: A 512 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7601 (mttm) REVERT: A 659 ASP cc_start: 0.7814 (m-30) cc_final: 0.7403 (m-30) REVERT: A 717 ASN cc_start: 0.7514 (t0) cc_final: 0.6588 (t0) REVERT: A 736 ASN cc_start: 0.7685 (t0) cc_final: 0.7341 (t0) REVERT: B 62 TYR cc_start: 0.7440 (m-80) cc_final: 0.6999 (m-80) REVERT: B 90 TYR cc_start: 0.8362 (m-80) cc_final: 0.7405 (m-80) REVERT: B 110 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7195 (mmtm) REVERT: B 130 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6302 (tm-30) REVERT: C 29 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: C 59 LYS cc_start: 0.8105 (pttm) cc_final: 0.7713 (tptp) REVERT: C 168 GLU cc_start: 0.7061 (pp20) cc_final: 0.6801 (pp20) REVERT: C 299 ARG cc_start: 0.6887 (mtp85) cc_final: 0.5959 (tpt170) REVERT: C 506 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6454 (mp0) REVERT: D 28 GLU cc_start: 0.6934 (tt0) cc_final: 0.6709 (tt0) REVERT: D 130 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6666 (tp30) REVERT: E 29 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: E 59 LYS cc_start: 0.8104 (pttm) cc_final: 0.7713 (tptp) REVERT: E 299 ARG cc_start: 0.6885 (mtp85) cc_final: 0.5956 (tpt170) REVERT: E 506 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6450 (mp0) REVERT: F 28 GLU cc_start: 0.6929 (tt0) cc_final: 0.6703 (tt0) REVERT: F 130 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6666 (tp30) REVERT: G 299 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6860 (ttp80) REVERT: G 343 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: G 347 GLU cc_start: 0.8141 (pt0) cc_final: 0.7783 (pt0) REVERT: G 425 ASP cc_start: 0.7008 (m-30) cc_final: 0.6628 (m-30) REVERT: G 447 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6899 (tmm-80) REVERT: G 491 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: G 506 GLU cc_start: 0.7300 (tt0) cc_final: 0.6390 (tp30) REVERT: G 512 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7599 (mttm) REVERT: G 659 ASP cc_start: 0.7819 (m-30) cc_final: 0.7408 (m-30) REVERT: G 717 ASN cc_start: 0.7514 (t0) cc_final: 0.6588 (t0) REVERT: G 736 ASN cc_start: 0.7686 (t0) cc_final: 0.7342 (t0) REVERT: H 21 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: H 62 TYR cc_start: 0.7440 (m-80) cc_final: 0.6999 (m-80) REVERT: H 90 TYR cc_start: 0.8401 (m-80) cc_final: 0.7434 (m-80) REVERT: H 110 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7198 (mmtm) REVERT: H 130 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6263 (tm-30) outliers start: 44 outliers final: 28 residues processed: 323 average time/residue: 1.7601 time to fit residues: 657.7826 Evaluate side-chains 338 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 350 optimal weight: 0.1980 chunk 322 optimal weight: 5.9990 chunk 279 optimal weight: 0.0970 chunk 28 optimal weight: 10.0000 chunk 215 optimal weight: 0.6980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29210 Z= 0.187 Angle : 0.532 9.303 39714 Z= 0.286 Chirality : 0.045 0.171 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.526 23.532 4010 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.53 % Allowed : 10.79 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3550 helix: 2.07 (0.20), residues: 656 sheet: 0.48 (0.20), residues: 728 loop : -0.02 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 101 HIS 0.005 0.001 HIS C 97 PHE 0.013 0.002 PHE C 713 TYR 0.025 0.001 TYR G 661 ARG 0.004 0.000 ARG G 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 302 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7503 (mptm) REVERT: A 299 ARG cc_start: 0.7188 (ttp-170) cc_final: 0.6859 (ttp80) REVERT: A 343 GLU cc_start: 0.7171 (tp30) cc_final: 0.6955 (tm-30) REVERT: A 347 GLU cc_start: 0.8139 (pt0) cc_final: 0.7795 (pt0) REVERT: A 425 ASP cc_start: 0.7060 (m-30) cc_final: 0.6719 (m-30) REVERT: A 447 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6868 (tmm-80) REVERT: A 491 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: A 506 GLU cc_start: 0.7255 (tt0) cc_final: 0.6348 (tp30) REVERT: A 512 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7520 (mttm) REVERT: A 659 ASP cc_start: 0.7775 (m-30) cc_final: 0.7389 (m-30) REVERT: A 717 ASN cc_start: 0.7508 (t0) cc_final: 0.6583 (t0) REVERT: A 736 ASN cc_start: 0.7669 (t0) cc_final: 0.7326 (t0) REVERT: B 62 TYR cc_start: 0.7423 (m-80) cc_final: 0.6997 (m-80) REVERT: B 90 TYR cc_start: 0.8361 (m-80) cc_final: 0.7414 (m-80) REVERT: B 110 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7208 (mmtm) REVERT: C 29 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: C 59 LYS cc_start: 0.8109 (pttm) cc_final: 0.7713 (tptp) REVERT: C 129 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6499 (mm-30) REVERT: C 168 GLU cc_start: 0.7183 (pp20) cc_final: 0.6917 (pp20) REVERT: C 299 ARG cc_start: 0.6895 (mtp85) cc_final: 0.5966 (tpt170) REVERT: C 506 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6448 (mp0) REVERT: D 28 GLU cc_start: 0.7103 (tt0) cc_final: 0.6878 (tt0) REVERT: D 130 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6661 (tp30) REVERT: E 29 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: E 31 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7283 (ttm110) REVERT: E 59 LYS cc_start: 0.8107 (pttm) cc_final: 0.7713 (tptp) REVERT: E 129 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6507 (mm-30) REVERT: E 299 ARG cc_start: 0.6892 (mtp85) cc_final: 0.5963 (tpt170) REVERT: E 506 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6446 (mp0) REVERT: F 28 GLU cc_start: 0.7097 (tt0) cc_final: 0.6873 (tt0) REVERT: F 130 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6661 (tp30) REVERT: G 59 LYS cc_start: 0.7907 (mppt) cc_final: 0.7505 (mptm) REVERT: G 299 ARG cc_start: 0.7189 (ttp-170) cc_final: 0.6861 (ttp80) REVERT: G 343 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: G 347 GLU cc_start: 0.8139 (pt0) cc_final: 0.7790 (pt0) REVERT: G 425 ASP cc_start: 0.7064 (m-30) cc_final: 0.6722 (m-30) REVERT: G 447 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6870 (tmm-80) REVERT: G 491 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: G 506 GLU cc_start: 0.7250 (tt0) cc_final: 0.6347 (tp30) REVERT: G 512 LYS cc_start: 0.7771 (mmtp) cc_final: 0.7519 (mttm) REVERT: G 659 ASP cc_start: 0.7807 (m-30) cc_final: 0.7414 (m-30) REVERT: G 717 ASN cc_start: 0.7507 (t0) cc_final: 0.6582 (t0) REVERT: G 736 ASN cc_start: 0.7670 (t0) cc_final: 0.7326 (t0) REVERT: H 21 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7440 (m-30) REVERT: H 62 TYR cc_start: 0.7412 (m-80) cc_final: 0.6982 (m-80) REVERT: H 90 TYR cc_start: 0.8398 (m-80) cc_final: 0.7430 (m-80) REVERT: H 110 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7195 (mmtm) outliers start: 37 outliers final: 26 residues processed: 322 average time/residue: 1.7044 time to fit residues: 628.6716 Evaluate side-chains 332 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 512 LYS Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 512 LYS Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 40 GLU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 343 GLU Chi-restraints excluded: chain G residue 445 ASP Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 689 ASP Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 297 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 279 optimal weight: 0.3980 chunk 117 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** G 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.100671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.082884 restraints weight = 106393.858| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.57 r_work: 0.2700 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 29210 Z= 0.225 Angle : 0.560 9.319 39714 Z= 0.301 Chirality : 0.046 0.173 4022 Planarity : 0.005 0.041 5284 Dihedral : 4.641 23.757 4010 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 10.42 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3550 helix: 2.02 (0.20), residues: 656 sheet: 0.34 (0.20), residues: 756 loop : -0.06 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 473 HIS 0.005 0.001 HIS C 97 PHE 0.015 0.002 PHE A 187 TYR 0.027 0.002 TYR A 661 ARG 0.003 0.000 ARG A 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10495.42 seconds wall clock time: 187 minutes 23.56 seconds (11243.56 seconds total)