Starting phenix.real_space_refine on Mon Mar 25 06:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orb_17119/03_2024/8orb_17119_neut.pdb" } resolution = 3.25 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= 0.017 sd= 0.157 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 29376 2.51 5 N 7992 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "E PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "F PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "G PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 625": "NH1" <-> "NH2" Residue "H PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 625": "NH1" <-> "NH2" Residue "I PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 625": "NH1" <-> "NH2" Residue "J PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 625": "NH1" <-> "NH2" Residue "K PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 625": "NH1" <-> "NH2" Residue "L PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 625": "NH1" <-> "NH2" Residue "M PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 625": "NH1" <-> "NH2" Residue "N PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 625": "NH1" <-> "NH2" Residue "O PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 625": "NH1" <-> "NH2" Residue "P PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 625": "NH1" <-> "NH2" Residue "Q PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 625": "NH1" <-> "NH2" Residue "R PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 625": "NH1" <-> "NH2" Residue "S PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 625": "NH1" <-> "NH2" Residue "T PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 625": "NH1" <-> "NH2" Residue "V PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 625": "NH1" <-> "NH2" Residue "W PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 625": "NH1" <-> "NH2" Residue "X PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 625": "NH1" <-> "NH2" Residue "Y PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 625": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45984 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "B" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "C" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "D" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "E" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "F" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "G" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "H" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "I" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "J" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "K" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "L" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "M" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "N" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "O" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "P" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "Q" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "R" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "S" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "T" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "V" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "W" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "X" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Chain: "Y" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1916 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 234} Time building chain proxies: 24.23, per 1000 atoms: 0.53 Number of scatterers: 45984 At special positions: 0 Unit cell: (147.65, 147.65, 147.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 8376 8.00 N 7992 7.00 C 29376 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: 18.10 Conformation dependent library (CDL) restraints added in 7.9 seconds 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 120 sheets defined 43.7% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS A 516 " --> pdb=" O VAL A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 517 through 534 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 405 through 422 Processing helix chain 'B' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 517 through 534 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 405 through 422 Processing helix chain 'C' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 450 " --> pdb=" O GLU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS C 516 " --> pdb=" O VAL C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 516' Processing helix chain 'C' and resid 517 through 534 Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 396 Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 450 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE D 461 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 516' Processing helix chain 'D' and resid 517 through 534 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 450 " --> pdb=" O GLU E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS E 516 " --> pdb=" O VAL E 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 513 through 516' Processing helix chain 'E' and resid 517 through 534 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 606 through 623 Processing helix chain 'E' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG F 450 " --> pdb=" O GLU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE F 461 " --> pdb=" O THR F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS F 516 " --> pdb=" O VAL F 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 513 through 516' Processing helix chain 'F' and resid 517 through 534 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 606 through 623 Processing helix chain 'F' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 396 Processing helix chain 'G' and resid 405 through 422 Processing helix chain 'G' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 450 " --> pdb=" O GLU G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE G 461 " --> pdb=" O THR G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS G 516 " --> pdb=" O VAL G 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 513 through 516' Processing helix chain 'G' and resid 517 through 534 Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 606 through 623 Processing helix chain 'G' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL G 628 " --> pdb=" O ARG G 625 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 396 Processing helix chain 'H' and resid 405 through 422 Processing helix chain 'H' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 450 " --> pdb=" O GLU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE H 461 " --> pdb=" O THR H 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS H 516 " --> pdb=" O VAL H 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 513 through 516' Processing helix chain 'H' and resid 517 through 534 Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 606 through 623 Processing helix chain 'H' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL H 628 " --> pdb=" O ARG H 625 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 396 Processing helix chain 'I' and resid 405 through 422 Processing helix chain 'I' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG I 450 " --> pdb=" O GLU I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE I 461 " --> pdb=" O THR I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS I 516 " --> pdb=" O VAL I 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 513 through 516' Processing helix chain 'I' and resid 517 through 534 Processing helix chain 'I' and resid 538 through 542 Processing helix chain 'I' and resid 606 through 623 Processing helix chain 'I' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL I 628 " --> pdb=" O ARG I 625 " (cutoff:3.500A) Processing helix chain 'J' and resid 392 through 396 Processing helix chain 'J' and resid 405 through 422 Processing helix chain 'J' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG J 450 " --> pdb=" O GLU J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE J 461 " --> pdb=" O THR J 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS J 516 " --> pdb=" O VAL J 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 513 through 516' Processing helix chain 'J' and resid 517 through 534 Processing helix chain 'J' and resid 538 through 542 Processing helix chain 'J' and resid 606 through 623 Processing helix chain 'J' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL J 628 " --> pdb=" O ARG J 625 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 396 Processing helix chain 'K' and resid 405 through 422 Processing helix chain 'K' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS K 449 " --> pdb=" O GLU K 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 450 " --> pdb=" O GLU K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE K 461 " --> pdb=" O THR K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS K 516 " --> pdb=" O VAL K 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 513 through 516' Processing helix chain 'K' and resid 517 through 534 Processing helix chain 'K' and resid 538 through 542 Processing helix chain 'K' and resid 606 through 623 Processing helix chain 'K' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL K 628 " --> pdb=" O ARG K 625 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 396 Processing helix chain 'L' and resid 405 through 422 Processing helix chain 'L' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS L 449 " --> pdb=" O GLU L 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG L 450 " --> pdb=" O GLU L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE L 461 " --> pdb=" O THR L 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS L 516 " --> pdb=" O VAL L 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 513 through 516' Processing helix chain 'L' and resid 517 through 534 Processing helix chain 'L' and resid 538 through 542 Processing helix chain 'L' and resid 606 through 623 Processing helix chain 'L' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL L 628 " --> pdb=" O ARG L 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 396 Processing helix chain 'M' and resid 405 through 422 Processing helix chain 'M' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS M 449 " --> pdb=" O GLU M 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG M 450 " --> pdb=" O GLU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE M 461 " --> pdb=" O THR M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS M 516 " --> pdb=" O VAL M 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 513 through 516' Processing helix chain 'M' and resid 517 through 534 Processing helix chain 'M' and resid 538 through 542 Processing helix chain 'M' and resid 606 through 623 Processing helix chain 'M' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL M 628 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 396 Processing helix chain 'N' and resid 405 through 422 Processing helix chain 'N' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS N 449 " --> pdb=" O GLU N 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 450 " --> pdb=" O GLU N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE N 461 " --> pdb=" O THR N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS N 516 " --> pdb=" O VAL N 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 513 through 516' Processing helix chain 'N' and resid 517 through 534 Processing helix chain 'N' and resid 538 through 542 Processing helix chain 'N' and resid 606 through 623 Processing helix chain 'N' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL N 628 " --> pdb=" O ARG N 625 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 396 Processing helix chain 'O' and resid 405 through 422 Processing helix chain 'O' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS O 449 " --> pdb=" O GLU O 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG O 450 " --> pdb=" O GLU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE O 461 " --> pdb=" O THR O 457 " (cutoff:3.500A) Processing helix chain 'O' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS O 516 " --> pdb=" O VAL O 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 513 through 516' Processing helix chain 'O' and resid 517 through 534 Processing helix chain 'O' and resid 538 through 542 Processing helix chain 'O' and resid 606 through 623 Processing helix chain 'O' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL O 628 " --> pdb=" O ARG O 625 " (cutoff:3.500A) Processing helix chain 'P' and resid 392 through 396 Processing helix chain 'P' and resid 405 through 422 Processing helix chain 'P' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS P 449 " --> pdb=" O GLU P 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG P 450 " --> pdb=" O GLU P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE P 461 " --> pdb=" O THR P 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS P 516 " --> pdb=" O VAL P 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 513 through 516' Processing helix chain 'P' and resid 517 through 534 Processing helix chain 'P' and resid 538 through 542 Processing helix chain 'P' and resid 606 through 623 Processing helix chain 'P' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL P 628 " --> pdb=" O ARG P 625 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 396 Processing helix chain 'Q' and resid 405 through 422 Processing helix chain 'Q' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS Q 449 " --> pdb=" O GLU Q 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Q 450 " --> pdb=" O GLU Q 446 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE Q 461 " --> pdb=" O THR Q 457 " (cutoff:3.500A) Processing helix chain 'Q' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS Q 516 " --> pdb=" O VAL Q 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 513 through 516' Processing helix chain 'Q' and resid 517 through 534 Processing helix chain 'Q' and resid 538 through 542 Processing helix chain 'Q' and resid 606 through 623 Processing helix chain 'Q' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL Q 628 " --> pdb=" O ARG Q 625 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 396 Processing helix chain 'R' and resid 405 through 422 Processing helix chain 'R' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS R 449 " --> pdb=" O GLU R 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG R 450 " --> pdb=" O GLU R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE R 461 " --> pdb=" O THR R 457 " (cutoff:3.500A) Processing helix chain 'R' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS R 516 " --> pdb=" O VAL R 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 513 through 516' Processing helix chain 'R' and resid 517 through 534 Processing helix chain 'R' and resid 538 through 542 Processing helix chain 'R' and resid 606 through 623 Processing helix chain 'R' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL R 628 " --> pdb=" O ARG R 625 " (cutoff:3.500A) Processing helix chain 'S' and resid 392 through 396 Processing helix chain 'S' and resid 405 through 422 Processing helix chain 'S' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS S 449 " --> pdb=" O GLU S 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG S 450 " --> pdb=" O GLU S 446 " (cutoff:3.500A) Processing helix chain 'S' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE S 461 " --> pdb=" O THR S 457 " (cutoff:3.500A) Processing helix chain 'S' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS S 516 " --> pdb=" O VAL S 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 513 through 516' Processing helix chain 'S' and resid 517 through 534 Processing helix chain 'S' and resid 538 through 542 Processing helix chain 'S' and resid 606 through 623 Processing helix chain 'S' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL S 628 " --> pdb=" O ARG S 625 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 396 Processing helix chain 'T' and resid 405 through 422 Processing helix chain 'T' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS T 449 " --> pdb=" O GLU T 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG T 450 " --> pdb=" O GLU T 446 " (cutoff:3.500A) Processing helix chain 'T' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE T 461 " --> pdb=" O THR T 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS T 516 " --> pdb=" O VAL T 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 513 through 516' Processing helix chain 'T' and resid 517 through 534 Processing helix chain 'T' and resid 538 through 542 Processing helix chain 'T' and resid 606 through 623 Processing helix chain 'T' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL T 628 " --> pdb=" O ARG T 625 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 396 Processing helix chain 'V' and resid 405 through 422 Processing helix chain 'V' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS V 449 " --> pdb=" O GLU V 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG V 450 " --> pdb=" O GLU V 446 " (cutoff:3.500A) Processing helix chain 'V' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE V 461 " --> pdb=" O THR V 457 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS V 516 " --> pdb=" O VAL V 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 516' Processing helix chain 'V' and resid 517 through 534 Processing helix chain 'V' and resid 538 through 542 Processing helix chain 'V' and resid 606 through 623 Processing helix chain 'V' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL V 628 " --> pdb=" O ARG V 625 " (cutoff:3.500A) Processing helix chain 'W' and resid 392 through 396 Processing helix chain 'W' and resid 405 through 422 Processing helix chain 'W' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS W 449 " --> pdb=" O GLU W 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG W 450 " --> pdb=" O GLU W 446 " (cutoff:3.500A) Processing helix chain 'W' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE W 461 " --> pdb=" O THR W 457 " (cutoff:3.500A) Processing helix chain 'W' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS W 516 " --> pdb=" O VAL W 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 513 through 516' Processing helix chain 'W' and resid 517 through 534 Processing helix chain 'W' and resid 538 through 542 Processing helix chain 'W' and resid 606 through 623 Processing helix chain 'W' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL W 628 " --> pdb=" O ARG W 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 392 through 396 Processing helix chain 'X' and resid 405 through 422 Processing helix chain 'X' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS X 449 " --> pdb=" O GLU X 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG X 450 " --> pdb=" O GLU X 446 " (cutoff:3.500A) Processing helix chain 'X' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE X 461 " --> pdb=" O THR X 457 " (cutoff:3.500A) Processing helix chain 'X' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS X 516 " --> pdb=" O VAL X 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 513 through 516' Processing helix chain 'X' and resid 517 through 534 Processing helix chain 'X' and resid 538 through 542 Processing helix chain 'X' and resid 606 through 623 Processing helix chain 'X' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL X 628 " --> pdb=" O ARG X 625 " (cutoff:3.500A) Processing helix chain 'Y' and resid 392 through 396 Processing helix chain 'Y' and resid 405 through 422 Processing helix chain 'Y' and resid 434 through 451 removed outlier: 3.773A pdb=" N LYS Y 449 " --> pdb=" O GLU Y 445 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Y 450 " --> pdb=" O GLU Y 446 " (cutoff:3.500A) Processing helix chain 'Y' and resid 457 through 473 removed outlier: 3.975A pdb=" N PHE Y 461 " --> pdb=" O THR Y 457 " (cutoff:3.500A) Processing helix chain 'Y' and resid 513 through 516 removed outlier: 3.938A pdb=" N LYS Y 516 " --> pdb=" O VAL Y 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 513 through 516' Processing helix chain 'Y' and resid 517 through 534 Processing helix chain 'Y' and resid 538 through 542 Processing helix chain 'Y' and resid 606 through 623 Processing helix chain 'Y' and resid 624 through 628 removed outlier: 3.555A pdb=" N VAL Y 628 " --> pdb=" O ARG Y 625 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR A 548 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 574 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 550 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR A 548 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 574 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER A 550 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 478 through 480 Processing sheet with id=AA5, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AA7, first strand: chain 'A' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR G 548 " --> pdb=" O LEU G 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL G 574 " --> pdb=" O THR G 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER G 550 " --> pdb=" O VAL G 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 403 Processing sheet with id=AB1, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR B 548 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 574 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 550 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR B 548 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 574 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER B 550 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 478 through 480 Processing sheet with id=AB4, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AB5, first strand: chain 'B' and resid 499 through 501 Processing sheet with id=AB6, first strand: chain 'B' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR M 548 " --> pdb=" O LEU M 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL M 574 " --> pdb=" O THR M 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER M 550 " --> pdb=" O VAL M 574 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 559 through 560 Processing sheet with id=AB8, first strand: chain 'C' and resid 399 through 403 Processing sheet with id=AB9, first strand: chain 'C' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR C 548 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 574 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 550 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR C 548 " --> pdb=" O LEU C 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 574 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 550 " --> pdb=" O VAL C 574 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 478 through 480 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC4, first strand: chain 'C' and resid 499 through 501 Processing sheet with id=AC5, first strand: chain 'C' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR P 548 " --> pdb=" O LEU P 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL P 574 " --> pdb=" O THR P 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER P 550 " --> pdb=" O VAL P 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 559 through 560 Processing sheet with id=AC7, first strand: chain 'D' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR D 548 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 574 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 550 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR D 548 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 574 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER D 550 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 478 through 480 Processing sheet with id=AD1, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AD2, first strand: chain 'D' and resid 499 through 501 Processing sheet with id=AD3, first strand: chain 'E' and resid 399 through 403 Processing sheet with id=AD4, first strand: chain 'E' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR E 548 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 574 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER E 550 " --> pdb=" O VAL E 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR E 548 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 574 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER E 550 " --> pdb=" O VAL E 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 478 through 480 Processing sheet with id=AD7, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'E' and resid 499 through 501 Processing sheet with id=AD9, first strand: chain 'E' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR W 548 " --> pdb=" O LEU W 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL W 574 " --> pdb=" O THR W 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER W 550 " --> pdb=" O VAL W 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 559 through 560 Processing sheet with id=AE2, first strand: chain 'F' and resid 399 through 403 Processing sheet with id=AE3, first strand: chain 'F' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR F 548 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 574 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER F 550 " --> pdb=" O VAL F 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR F 548 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 574 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER F 550 " --> pdb=" O VAL F 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 478 through 480 Processing sheet with id=AE6, first strand: chain 'F' and resid 494 through 496 Processing sheet with id=AE7, first strand: chain 'F' and resid 499 through 501 Processing sheet with id=AE8, first strand: chain 'F' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR H 548 " --> pdb=" O LEU H 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL H 574 " --> pdb=" O THR H 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER H 550 " --> pdb=" O VAL H 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 559 through 560 Processing sheet with id=AF1, first strand: chain 'G' and resid 494 through 496 Processing sheet with id=AF2, first strand: chain 'G' and resid 499 through 501 Processing sheet with id=AF3, first strand: chain 'H' and resid 399 through 403 Processing sheet with id=AF4, first strand: chain 'H' and resid 494 through 496 Processing sheet with id=AF5, first strand: chain 'H' and resid 499 through 501 Processing sheet with id=AF6, first strand: chain 'H' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR X 548 " --> pdb=" O LEU X 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL X 574 " --> pdb=" O THR X 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER X 550 " --> pdb=" O VAL X 574 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 559 through 560 Processing sheet with id=AF8, first strand: chain 'I' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR I 548 " --> pdb=" O LEU I 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL I 574 " --> pdb=" O THR I 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER I 550 " --> pdb=" O VAL I 574 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR I 548 " --> pdb=" O LEU I 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL I 574 " --> pdb=" O THR I 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER I 550 " --> pdb=" O VAL I 574 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 478 through 480 Processing sheet with id=AG2, first strand: chain 'I' and resid 494 through 496 Processing sheet with id=AG3, first strand: chain 'I' and resid 499 through 501 Processing sheet with id=AG4, first strand: chain 'J' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR J 548 " --> pdb=" O LEU J 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL J 574 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER J 550 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR J 548 " --> pdb=" O LEU J 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL J 574 " --> pdb=" O THR J 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER J 550 " --> pdb=" O VAL J 574 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 478 through 480 Processing sheet with id=AG7, first strand: chain 'J' and resid 494 through 496 Processing sheet with id=AG8, first strand: chain 'J' and resid 499 through 501 Processing sheet with id=AG9, first strand: chain 'K' and resid 399 through 403 Processing sheet with id=AH1, first strand: chain 'K' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR K 548 " --> pdb=" O LEU K 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL K 574 " --> pdb=" O THR K 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER K 550 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR K 548 " --> pdb=" O LEU K 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL K 574 " --> pdb=" O THR K 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER K 550 " --> pdb=" O VAL K 574 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 478 through 480 Processing sheet with id=AH4, first strand: chain 'K' and resid 494 through 496 Processing sheet with id=AH5, first strand: chain 'K' and resid 499 through 501 Processing sheet with id=AH6, first strand: chain 'K' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR Q 548 " --> pdb=" O LEU Q 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Q 574 " --> pdb=" O THR Q 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER Q 550 " --> pdb=" O VAL Q 574 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 559 through 560 Processing sheet with id=AH8, first strand: chain 'L' and resid 399 through 403 Processing sheet with id=AH9, first strand: chain 'L' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR L 548 " --> pdb=" O LEU L 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL L 574 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER L 550 " --> pdb=" O VAL L 574 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR L 548 " --> pdb=" O LEU L 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL L 574 " --> pdb=" O THR L 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER L 550 " --> pdb=" O VAL L 574 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 478 through 480 Processing sheet with id=AI3, first strand: chain 'L' and resid 494 through 496 Processing sheet with id=AI4, first strand: chain 'L' and resid 499 through 501 Processing sheet with id=AI5, first strand: chain 'L' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR N 548 " --> pdb=" O LEU N 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL N 574 " --> pdb=" O THR N 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER N 550 " --> pdb=" O VAL N 574 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 559 through 560 Processing sheet with id=AI7, first strand: chain 'M' and resid 494 through 496 Processing sheet with id=AI8, first strand: chain 'M' and resid 499 through 501 Processing sheet with id=AI9, first strand: chain 'N' and resid 399 through 403 Processing sheet with id=AJ1, first strand: chain 'N' and resid 494 through 496 Processing sheet with id=AJ2, first strand: chain 'N' and resid 499 through 501 Processing sheet with id=AJ3, first strand: chain 'N' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR R 548 " --> pdb=" O LEU R 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL R 574 " --> pdb=" O THR R 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER R 550 " --> pdb=" O VAL R 574 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'N' and resid 559 through 560 Processing sheet with id=AJ5, first strand: chain 'O' and resid 399 through 403 Processing sheet with id=AJ6, first strand: chain 'O' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR O 548 " --> pdb=" O LEU O 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL O 574 " --> pdb=" O THR O 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER O 550 " --> pdb=" O VAL O 574 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR O 548 " --> pdb=" O LEU O 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL O 574 " --> pdb=" O THR O 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER O 550 " --> pdb=" O VAL O 574 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 478 through 480 Processing sheet with id=AJ9, first strand: chain 'O' and resid 494 through 496 Processing sheet with id=AK1, first strand: chain 'O' and resid 499 through 501 Processing sheet with id=AK2, first strand: chain 'O' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR T 548 " --> pdb=" O LEU T 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL T 574 " --> pdb=" O THR T 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER T 550 " --> pdb=" O VAL T 574 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'O' and resid 559 through 560 Processing sheet with id=AK4, first strand: chain 'P' and resid 494 through 496 Processing sheet with id=AK5, first strand: chain 'P' and resid 499 through 501 Processing sheet with id=AK6, first strand: chain 'Q' and resid 399 through 403 Processing sheet with id=AK7, first strand: chain 'Q' and resid 494 through 496 Processing sheet with id=AK8, first strand: chain 'Q' and resid 499 through 501 Processing sheet with id=AK9, first strand: chain 'Q' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR V 548 " --> pdb=" O LEU V 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL V 574 " --> pdb=" O THR V 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER V 550 " --> pdb=" O VAL V 574 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 559 through 560 Processing sheet with id=AL2, first strand: chain 'R' and resid 494 through 496 Processing sheet with id=AL3, first strand: chain 'R' and resid 499 through 501 Processing sheet with id=AL4, first strand: chain 'S' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR S 548 " --> pdb=" O LEU S 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL S 574 " --> pdb=" O THR S 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER S 550 " --> pdb=" O VAL S 574 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'S' and resid 548 through 551 removed outlier: 6.581A pdb=" N THR S 548 " --> pdb=" O LEU S 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL S 574 " --> pdb=" O THR S 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER S 550 " --> pdb=" O VAL S 574 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'S' and resid 478 through 480 Processing sheet with id=AL7, first strand: chain 'S' and resid 494 through 496 Processing sheet with id=AL8, first strand: chain 'S' and resid 499 through 501 Processing sheet with id=AL9, first strand: chain 'T' and resid 399 through 403 Processing sheet with id=AM1, first strand: chain 'T' and resid 494 through 496 Processing sheet with id=AM2, first strand: chain 'T' and resid 499 through 501 Processing sheet with id=AM3, first strand: chain 'T' and resid 559 through 560 removed outlier: 6.581A pdb=" N THR Y 548 " --> pdb=" O LEU Y 572 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Y 574 " --> pdb=" O THR Y 548 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER Y 550 " --> pdb=" O VAL Y 574 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'T' and resid 559 through 560 Processing sheet with id=AM5, first strand: chain 'V' and resid 494 through 496 Processing sheet with id=AM6, first strand: chain 'V' and resid 499 through 501 Processing sheet with id=AM7, first strand: chain 'W' and resid 494 through 496 Processing sheet with id=AM8, first strand: chain 'W' and resid 499 through 501 Processing sheet with id=AM9, first strand: chain 'X' and resid 494 through 496 Processing sheet with id=AN1, first strand: chain 'X' and resid 499 through 501 Processing sheet with id=AN2, first strand: chain 'Y' and resid 494 through 496 Processing sheet with id=AN3, first strand: chain 'Y' and resid 499 through 501 2568 hydrogen bonds defined for protein. 6912 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: 19.73 Time building geometry restraints manager: 19.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15096 1.34 - 1.46: 8196 1.46 - 1.58: 23076 1.58 - 1.69: 0 1.69 - 1.81: 456 Bond restraints: 46824 Sorted by residual: bond pdb=" CA PHE W 547 " pdb=" C PHE W 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE O 547 " pdb=" C PHE O 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE S 547 " pdb=" C PHE S 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE G 547 " pdb=" C PHE G 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 bond pdb=" CA PHE K 547 " pdb=" C PHE K 547 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.18e+00 ... (remaining 46819 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.22: 1776 107.22 - 113.91: 27288 113.91 - 120.60: 17400 120.60 - 127.29: 16296 127.29 - 133.99: 432 Bond angle restraints: 63192 Sorted by residual: angle pdb=" NE ARG L 625 " pdb=" CZ ARG L 625 " pdb=" NH2 ARG L 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG S 625 " pdb=" CZ ARG S 625 " pdb=" NH2 ARG S 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG E 625 " pdb=" CZ ARG E 625 " pdb=" NH2 ARG E 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG A 625 " pdb=" CZ ARG A 625 " pdb=" NH2 ARG A 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 angle pdb=" NE ARG K 625 " pdb=" CZ ARG K 625 " pdb=" NH2 ARG K 625 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.70e+00 ... (remaining 63187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.28: 27096 11.28 - 22.56: 1224 22.56 - 33.83: 216 33.83 - 45.11: 72 45.11 - 56.39: 96 Dihedral angle restraints: 28704 sinusoidal: 11832 harmonic: 16872 Sorted by residual: dihedral pdb=" CA LYS B 455 " pdb=" CB LYS B 455 " pdb=" CG LYS B 455 " pdb=" CD LYS B 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA LYS N 455 " pdb=" CB LYS N 455 " pdb=" CG LYS N 455 " pdb=" CD LYS N 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CA LYS I 455 " pdb=" CB LYS I 455 " pdb=" CG LYS I 455 " pdb=" CD LYS I 455 " ideal model delta sinusoidal sigma weight residual -180.00 -123.61 -56.39 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 28701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 4272 0.025 - 0.050: 1872 0.050 - 0.075: 480 0.075 - 0.100: 432 0.100 - 0.125: 240 Chirality restraints: 7296 Sorted by residual: chirality pdb=" CA VAL V 425 " pdb=" N VAL V 425 " pdb=" C VAL V 425 " pdb=" CB VAL V 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL I 425 " pdb=" N VAL I 425 " pdb=" C VAL I 425 " pdb=" CB VAL I 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL T 425 " pdb=" N VAL T 425 " pdb=" C VAL T 425 " pdb=" CB VAL T 425 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 7293 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 501 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO N 502 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO N 502 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO N 502 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 501 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO M 502 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO M 502 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 502 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 501 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO G 502 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO G 502 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 502 " 0.015 5.00e-02 4.00e+02 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 14304 2.84 - 3.35: 41820 3.35 - 3.87: 76440 3.87 - 4.38: 87240 4.38 - 4.90: 152268 Nonbonded interactions: 372072 Sorted by model distance: nonbonded pdb=" O GLY B 556 " pdb=" OG1 THR B 557 " model vdw 2.322 2.440 nonbonded pdb=" O GLY Q 556 " pdb=" OG1 THR Q 557 " model vdw 2.322 2.440 nonbonded pdb=" O GLY L 556 " pdb=" OG1 THR L 557 " model vdw 2.322 2.440 nonbonded pdb=" O GLY A 556 " pdb=" OG1 THR A 557 " model vdw 2.322 2.440 nonbonded pdb=" O GLY O 556 " pdb=" OG1 THR O 557 " model vdw 2.322 2.440 ... (remaining 372067 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.040 Extract box with map and model: 5.770 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 115.790 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.430 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.002 0.017 46824 Z= 0.108 Angle : 0.416 3.915 63192 Z= 0.251 Chirality : 0.039 0.125 7296 Planarity : 0.004 0.028 8064 Dihedral : 7.781 56.389 17760 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.47 % Allowed : 3.79 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.12), residues: 5880 helix: 2.88 (0.11), residues: 2088 sheet: 0.03 (0.15), residues: 1392 loop : -0.04 (0.14), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 583 HIS 0.001 0.001 HIS S 559 PHE 0.009 0.001 PHE A 613 TYR 0.001 0.000 TYR P 492 ARG 0.001 0.000 ARG N 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 870 time to evaluate : 5.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8074 (mmm) REVERT: D 385 MET cc_start: 0.4596 (ptt) cc_final: 0.4299 (mmm) REVERT: H 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: I 385 MET cc_start: 0.4546 (ptt) cc_final: 0.4311 (mmm) REVERT: J 385 MET cc_start: 0.4593 (ptt) cc_final: 0.4311 (mmm) REVERT: J 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: K 593 MET cc_start: 0.8314 (mmm) cc_final: 0.8064 (mmm) REVERT: L 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8069 (mmm) REVERT: M 385 MET cc_start: 0.4563 (ptt) cc_final: 0.4324 (mmm) REVERT: O 593 MET cc_start: 0.8292 (mmm) cc_final: 0.8074 (mmm) REVERT: P 385 MET cc_start: 0.4551 (ptt) cc_final: 0.4319 (mmm) REVERT: R 385 MET cc_start: 0.4603 (ptt) cc_final: 0.4312 (mmm) REVERT: S 385 MET cc_start: 0.4633 (ptt) cc_final: 0.4313 (mmm) REVERT: V 385 MET cc_start: 0.4567 (ptt) cc_final: 0.4333 (mmm) REVERT: W 385 MET cc_start: 0.4636 (ptt) cc_final: 0.4317 (mmm) REVERT: X 385 MET cc_start: 0.4571 (ptt) cc_final: 0.4304 (mmm) REVERT: Y 385 MET cc_start: 0.4600 (ptt) cc_final: 0.4307 (mmm) outliers start: 24 outliers final: 0 residues processed: 894 average time/residue: 0.6425 time to fit residues: 897.4881 Evaluate side-chains 567 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 0.9990 chunk 436 optimal weight: 0.0870 chunk 242 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 451 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 HIS A 444 ASN B 427 HIS B 444 ASN B 559 HIS C 427 HIS C 444 ASN C 559 HIS D 427 HIS D 444 ASN D 559 HIS E 427 HIS E 444 ASN E 559 HIS F 427 HIS F 444 ASN G 427 HIS G 444 ASN H 427 HIS H 444 ASN I 427 HIS I 444 ASN I 559 HIS J 427 HIS J 444 ASN K 427 HIS K 444 ASN K 559 HIS L 427 HIS L 444 ASN M 427 HIS M 444 ASN M 559 HIS N 427 HIS N 444 ASN O 427 HIS O 444 ASN P 427 HIS P 444 ASN Q 427 HIS Q 444 ASN R 427 HIS R 444 ASN S 427 HIS S 444 ASN S 559 HIS T 427 HIS T 444 ASN V 427 HIS V 444 ASN W 427 HIS W 444 ASN X 427 HIS X 444 ASN Y 427 HIS Y 444 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 46824 Z= 0.160 Angle : 0.447 4.129 63192 Z= 0.239 Chirality : 0.041 0.125 7296 Planarity : 0.004 0.028 8064 Dihedral : 3.216 11.175 6240 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.02 % Favored : 98.78 % Rotamer: Outliers : 0.97 % Allowed : 6.52 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.11), residues: 5880 helix: 2.82 (0.11), residues: 2136 sheet: 0.27 (0.15), residues: 1152 loop : 0.02 (0.13), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.003 0.001 HIS N 559 PHE 0.010 0.002 PHE J 560 TYR 0.002 0.001 TYR L 492 ARG 0.005 0.001 ARG L 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 589 time to evaluate : 5.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 9 residues processed: 619 average time/residue: 0.5606 time to fit residues: 573.5360 Evaluate side-chains 524 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 515 time to evaluate : 5.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain X residue 528 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 435 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 524 optimal weight: 0.5980 chunk 566 optimal weight: 9.9990 chunk 466 optimal weight: 20.0000 chunk 519 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 420 optimal weight: 0.7980 overall best weight: 3.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 GLN ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** C 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN E 443 GLN ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 GLN G 443 GLN H 443 GLN ** H 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN J 443 GLN K 443 GLN L 443 GLN M 443 GLN ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 443 GLN ** N 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 443 GLN ** O 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 443 GLN ** P 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN ** Q 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 443 GLN S 443 GLN T 443 GLN ** T 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN W 443 GLN ** W 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 443 GLN Y 443 GLN ** Y 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 46824 Z= 0.378 Angle : 0.566 4.797 63192 Z= 0.303 Chirality : 0.046 0.129 7296 Planarity : 0.005 0.037 8064 Dihedral : 3.827 15.272 6240 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.86 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 7.50 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 5880 helix: 2.30 (0.11), residues: 2136 sheet: -0.06 (0.15), residues: 1152 loop : -0.30 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 583 HIS 0.004 0.001 HIS P 424 PHE 0.016 0.003 PHE D 560 TYR 0.004 0.001 TYR Y 492 ARG 0.004 0.001 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 529 time to evaluate : 5.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.5691 (mmm) cc_final: 0.5437 (ttp) REVERT: C 473 MET cc_start: 0.7536 (mtt) cc_final: 0.7231 (mtt) REVERT: D 473 MET cc_start: 0.7548 (mtt) cc_final: 0.7237 (mtt) REVERT: E 473 MET cc_start: 0.7548 (mtt) cc_final: 0.7216 (mtt) REVERT: F 473 MET cc_start: 0.7551 (mtt) cc_final: 0.7238 (mtt) REVERT: G 473 MET cc_start: 0.7543 (mtt) cc_final: 0.7214 (mtt) REVERT: H 473 MET cc_start: 0.7544 (mtt) cc_final: 0.7234 (mtt) REVERT: I 473 MET cc_start: 0.7548 (mtt) cc_final: 0.7241 (mtt) REVERT: J 473 MET cc_start: 0.7549 (mtt) cc_final: 0.7240 (mtt) REVERT: K 473 MET cc_start: 0.7550 (mtt) cc_final: 0.7245 (mtt) REVERT: L 385 MET cc_start: 0.5695 (mmm) cc_final: 0.5430 (ttp) REVERT: M 473 MET cc_start: 0.7542 (mtt) cc_final: 0.7224 (mtt) REVERT: N 385 MET cc_start: 0.6412 (mmm) cc_final: 0.5852 (mtp) REVERT: N 473 MET cc_start: 0.7545 (mtt) cc_final: 0.7215 (mtt) REVERT: O 385 MET cc_start: 0.5682 (mmm) cc_final: 0.5424 (ttp) REVERT: P 473 MET cc_start: 0.7543 (mtt) cc_final: 0.7237 (mtt) REVERT: R 473 MET cc_start: 0.7550 (mtt) cc_final: 0.7239 (mtt) REVERT: S 473 MET cc_start: 0.7549 (mtt) cc_final: 0.7218 (mtt) REVERT: T 385 MET cc_start: 0.6421 (mmm) cc_final: 0.5860 (mtp) REVERT: T 473 MET cc_start: 0.7545 (mtt) cc_final: 0.7216 (mtt) REVERT: V 473 MET cc_start: 0.7545 (mtt) cc_final: 0.7226 (mtt) REVERT: W 473 MET cc_start: 0.7548 (mtt) cc_final: 0.7217 (mtt) REVERT: Y 473 MET cc_start: 0.7552 (mtt) cc_final: 0.7242 (mtt) outliers start: 72 outliers final: 42 residues processed: 583 average time/residue: 0.5541 time to fit residues: 534.5250 Evaluate side-chains 531 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 489 time to evaluate : 4.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain G residue 503 ASN Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 503 ASN Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 503 ASN Chi-restraints excluded: chain N residue 503 ASN Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain V residue 503 ASN Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 351 optimal weight: 8.9990 chunk 525 optimal weight: 3.9990 chunk 556 optimal weight: 4.9990 chunk 274 optimal weight: 20.0000 chunk 498 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 46824 Z= 0.328 Angle : 0.525 4.505 63192 Z= 0.281 Chirality : 0.045 0.127 7296 Planarity : 0.005 0.042 8064 Dihedral : 3.798 13.684 6240 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.04 % Favored : 97.55 % Rotamer: Outliers : 1.54 % Allowed : 10.92 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.66 (0.11), residues: 5880 helix: 1.86 (0.11), residues: 2280 sheet: -0.23 (0.14), residues: 1152 loop : -0.54 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 583 HIS 0.003 0.001 HIS P 424 PHE 0.014 0.002 PHE D 560 TYR 0.004 0.001 TYR B 492 ARG 0.003 0.000 ARG W 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 511 time to evaluate : 5.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: B 473 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7176 (mtt) REVERT: C 473 MET cc_start: 0.7549 (mtt) cc_final: 0.7218 (mtt) REVERT: D 385 MET cc_start: 0.6291 (mmm) cc_final: 0.4301 (ptp) REVERT: D 473 MET cc_start: 0.7553 (mtt) cc_final: 0.7219 (mtt) REVERT: F 473 MET cc_start: 0.7557 (mtt) cc_final: 0.7224 (mtt) REVERT: G 385 MET cc_start: 0.6690 (mmm) cc_final: 0.6026 (mmm) REVERT: H 473 MET cc_start: 0.7552 (mtt) cc_final: 0.7214 (mtt) REVERT: I 385 MET cc_start: 0.6254 (mmm) cc_final: 0.4315 (ptp) REVERT: I 473 MET cc_start: 0.7550 (mtt) cc_final: 0.7217 (mtt) REVERT: J 385 MET cc_start: 0.6274 (mmm) cc_final: 0.4326 (ptp) REVERT: J 473 MET cc_start: 0.7547 (mtt) cc_final: 0.7216 (mtt) REVERT: K 473 MET cc_start: 0.7549 (mtt) cc_final: 0.7221 (mtt) REVERT: L 473 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7180 (mtt) REVERT: M 385 MET cc_start: 0.6350 (mmm) cc_final: 0.4383 (ptp) REVERT: M 473 MET cc_start: 0.7557 (mtt) cc_final: 0.7219 (mtt) REVERT: O 473 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: P 385 MET cc_start: 0.6342 (mmm) cc_final: 0.4390 (ptp) REVERT: P 473 MET cc_start: 0.7550 (mtt) cc_final: 0.7215 (mtt) REVERT: Q 473 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: R 385 MET cc_start: 0.6292 (mmm) cc_final: 0.4308 (ptp) REVERT: R 473 MET cc_start: 0.7556 (mtt) cc_final: 0.7222 (mtt) REVERT: S 385 MET cc_start: 0.6286 (mmm) cc_final: 0.4310 (ptp) REVERT: V 385 MET cc_start: 0.6284 (mmm) cc_final: 0.4326 (ptp) REVERT: V 473 MET cc_start: 0.7559 (mtt) cc_final: 0.7222 (mtt) REVERT: W 385 MET cc_start: 0.6372 (mmm) cc_final: 0.4401 (ptp) REVERT: X 385 MET cc_start: 0.6287 (mmm) cc_final: 0.4315 (ptp) REVERT: X 473 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7177 (mtt) REVERT: Y 385 MET cc_start: 0.6293 (mmm) cc_final: 0.4306 (ptp) REVERT: Y 473 MET cc_start: 0.7558 (mtt) cc_final: 0.7223 (mtt) outliers start: 78 outliers final: 60 residues processed: 559 average time/residue: 0.5575 time to fit residues: 518.4303 Evaluate side-chains 532 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 466 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 503 ASN Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 503 ASN Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 503 ASN Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 503 ASN Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 503 ASN Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 414 optimal weight: 0.0170 chunk 229 optimal weight: 10.0000 chunk 475 optimal weight: 0.9980 chunk 384 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 499 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 46824 Z= 0.115 Angle : 0.402 3.975 63192 Z= 0.215 Chirality : 0.040 0.126 7296 Planarity : 0.004 0.041 8064 Dihedral : 3.239 10.519 6240 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.41 % Allowed : 0.82 % Favored : 98.78 % Rotamer: Outliers : 1.15 % Allowed : 10.76 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 5880 helix: 2.33 (0.11), residues: 2280 sheet: 0.14 (0.15), residues: 1152 loop : -0.22 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 583 HIS 0.001 0.000 HIS H 559 PHE 0.012 0.001 PHE E 613 TYR 0.001 0.000 TYR E 492 ARG 0.004 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 527 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 385 MET cc_start: 0.6445 (mmm) cc_final: 0.4482 (ptp) REVERT: G 385 MET cc_start: 0.6550 (mmm) cc_final: 0.6055 (mmm) REVERT: I 385 MET cc_start: 0.6452 (mmm) cc_final: 0.4466 (ptp) REVERT: J 385 MET cc_start: 0.6454 (mmm) cc_final: 0.4479 (ptp) REVERT: M 385 MET cc_start: 0.6526 (mmm) cc_final: 0.4556 (ptp) REVERT: P 385 MET cc_start: 0.6519 (mmm) cc_final: 0.4558 (ptp) REVERT: R 385 MET cc_start: 0.6450 (mmm) cc_final: 0.4493 (ptp) REVERT: R 421 MET cc_start: 0.8314 (mtt) cc_final: 0.8024 (mtt) REVERT: S 385 MET cc_start: 0.6461 (mmm) cc_final: 0.4473 (ptp) REVERT: V 385 MET cc_start: 0.6471 (mmm) cc_final: 0.4484 (ptp) REVERT: W 385 MET cc_start: 0.6548 (mmm) cc_final: 0.4570 (ptp) REVERT: X 385 MET cc_start: 0.6460 (mmm) cc_final: 0.4482 (ptp) REVERT: Y 385 MET cc_start: 0.6450 (mmm) cc_final: 0.4491 (ptp) REVERT: Y 421 MET cc_start: 0.8316 (mtt) cc_final: 0.8023 (mtt) outliers start: 58 outliers final: 24 residues processed: 560 average time/residue: 0.5354 time to fit residues: 498.8339 Evaluate side-chains 490 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 466 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 3.9990 chunk 501 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 557 optimal weight: 4.9990 chunk 462 optimal weight: 4.9990 chunk 258 optimal weight: 0.0970 chunk 46 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 46824 Z= 0.357 Angle : 0.525 4.641 63192 Z= 0.282 Chirality : 0.045 0.130 7296 Planarity : 0.005 0.042 8064 Dihedral : 3.708 12.651 6240 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.86 % Favored : 96.73 % Rotamer: Outliers : 1.54 % Allowed : 11.53 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.86 (0.11), residues: 5880 helix: 2.09 (0.11), residues: 2280 sheet: -0.28 (0.14), residues: 1152 loop : -0.40 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 583 HIS 0.003 0.001 HIS M 424 PHE 0.016 0.002 PHE D 560 TYR 0.004 0.002 TYR B 492 ARG 0.003 0.000 ARG Y 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 492 time to evaluate : 5.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7123 (mtt) REVERT: B 473 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7115 (mtt) REVERT: D 385 MET cc_start: 0.6086 (mmm) cc_final: 0.4504 (ptp) REVERT: D 473 MET cc_start: 0.7624 (mtt) cc_final: 0.7324 (mtt) REVERT: F 473 MET cc_start: 0.7626 (mtt) cc_final: 0.7320 (mtt) REVERT: G 473 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: I 385 MET cc_start: 0.6448 (mmm) cc_final: 0.4342 (ptp) REVERT: J 385 MET cc_start: 0.6066 (mmm) cc_final: 0.4511 (ptp) REVERT: J 473 MET cc_start: 0.7618 (mtt) cc_final: 0.7320 (mtt) REVERT: K 473 MET cc_start: 0.7618 (mtt) cc_final: 0.7261 (mtt) REVERT: L 473 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7128 (mtt) REVERT: M 385 MET cc_start: 0.6196 (mmm) cc_final: 0.4675 (ptp) REVERT: M 473 MET cc_start: 0.7617 (mtt) cc_final: 0.7302 (mtt) REVERT: N 473 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7135 (mtt) REVERT: O 473 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7124 (mtt) REVERT: P 385 MET cc_start: 0.6527 (mmm) cc_final: 0.4438 (ptp) REVERT: Q 473 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7114 (mtt) REVERT: R 385 MET cc_start: 0.6092 (mmm) cc_final: 0.4510 (ptp) REVERT: R 421 MET cc_start: 0.8453 (mtt) cc_final: 0.8121 (mtt) REVERT: R 473 MET cc_start: 0.7624 (mtt) cc_final: 0.7326 (mtt) REVERT: S 385 MET cc_start: 0.6080 (mmm) cc_final: 0.4504 (ptp) REVERT: T 473 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: V 385 MET cc_start: 0.6136 (mmm) cc_final: 0.4605 (ptp) REVERT: V 473 MET cc_start: 0.7627 (mtt) cc_final: 0.7329 (mtt) REVERT: W 385 MET cc_start: 0.6162 (mmm) cc_final: 0.4600 (ptp) REVERT: X 385 MET cc_start: 0.6074 (mmm) cc_final: 0.4519 (ptp) REVERT: X 473 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7115 (mtt) REVERT: Y 385 MET cc_start: 0.6091 (mmm) cc_final: 0.4508 (ptp) REVERT: Y 421 MET cc_start: 0.8452 (mtt) cc_final: 0.8121 (mtt) REVERT: Y 473 MET cc_start: 0.7622 (mtt) cc_final: 0.7324 (mtt) outliers start: 78 outliers final: 48 residues processed: 528 average time/residue: 0.6160 time to fit residues: 546.0592 Evaluate side-chains 520 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 463 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 410 ILE Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 410 ILE Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 317 optimal weight: 1.9990 chunk 406 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 469 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 555 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 338 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 46824 Z= 0.444 Angle : 0.594 5.127 63192 Z= 0.319 Chirality : 0.047 0.138 7296 Planarity : 0.005 0.045 8064 Dihedral : 4.051 13.968 6240 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.50 % Favored : 97.09 % Rotamer: Outliers : 2.41 % Allowed : 12.24 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.43 (0.11), residues: 5880 helix: 1.77 (0.11), residues: 2280 sheet: -0.58 (0.14), residues: 1152 loop : -0.64 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP T 583 HIS 0.004 0.001 HIS N 424 PHE 0.017 0.003 PHE B 560 TYR 0.006 0.002 TYR C 492 ARG 0.003 0.000 ARG O 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 464 time to evaluate : 5.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7121 (mtt) REVERT: B 473 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7107 (mtt) REVERT: C 473 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: D 385 MET cc_start: 0.6284 (mmm) cc_final: 0.4683 (ptp) REVERT: D 473 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7230 (mtt) REVERT: E 473 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7125 (mtt) REVERT: F 473 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7240 (mtt) REVERT: G 473 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7144 (mtt) REVERT: H 473 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7186 (mtt) REVERT: I 385 MET cc_start: 0.6244 (mmm) cc_final: 0.4667 (ptp) REVERT: I 473 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: J 385 MET cc_start: 0.6261 (mmm) cc_final: 0.4674 (ptp) REVERT: J 473 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7228 (mtt) REVERT: K 473 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: L 473 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7123 (mtt) REVERT: M 385 MET cc_start: 0.6323 (mmm) cc_final: 0.4753 (ptp) REVERT: M 473 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: N 473 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7145 (mtt) REVERT: O 473 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7121 (mtt) REVERT: P 385 MET cc_start: 0.6318 (mmm) cc_final: 0.4752 (ptp) REVERT: P 473 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: Q 473 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7112 (mtt) REVERT: R 385 MET cc_start: 0.6287 (mmm) cc_final: 0.4693 (ptp) REVERT: R 421 MET cc_start: 0.8460 (mtt) cc_final: 0.8129 (mtt) REVERT: R 473 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: S 385 MET cc_start: 0.6283 (mmm) cc_final: 0.4676 (ptp) REVERT: S 473 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7139 (mtt) REVERT: T 473 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7133 (mtt) REVERT: V 385 MET cc_start: 0.6270 (mmm) cc_final: 0.4690 (ptp) REVERT: V 473 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7241 (mtt) REVERT: W 385 MET cc_start: 0.6354 (mmm) cc_final: 0.4763 (ptp) REVERT: W 473 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7135 (mtt) REVERT: X 385 MET cc_start: 0.6271 (mmm) cc_final: 0.4684 (ptp) REVERT: X 473 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7112 (mtt) REVERT: Y 385 MET cc_start: 0.6283 (mmm) cc_final: 0.4689 (ptp) REVERT: Y 421 MET cc_start: 0.8462 (mtt) cc_final: 0.8129 (mtt) REVERT: Y 473 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7232 (mtt) outliers start: 122 outliers final: 72 residues processed: 536 average time/residue: 0.5394 time to fit residues: 482.0790 Evaluate side-chains 553 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 457 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 503 ASN Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 503 ASN Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 503 ASN Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 503 ASN Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 410 ILE Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 503 ASN Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 410 ILE Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 352 optimal weight: 4.9990 chunk 378 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 436 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 442 GLN F 442 GLN H 442 GLN J 442 GLN K 442 GLN M 442 GLN V 442 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 46824 Z= 0.206 Angle : 0.456 4.306 63192 Z= 0.244 Chirality : 0.042 0.127 7296 Planarity : 0.004 0.044 8064 Dihedral : 3.602 11.211 6240 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.18 % Favored : 97.41 % Rotamer: Outliers : 1.97 % Allowed : 12.86 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.83 (0.11), residues: 5880 helix: 2.19 (0.11), residues: 2280 sheet: -0.39 (0.14), residues: 1152 loop : -0.51 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 583 HIS 0.002 0.001 HIS H 559 PHE 0.013 0.002 PHE X 613 TYR 0.003 0.001 TYR X 492 ARG 0.004 0.000 ARG K 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 501 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: B 473 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7211 (mtt) REVERT: C 473 MET cc_start: 0.7697 (mtt) cc_final: 0.7279 (mtt) REVERT: D 385 MET cc_start: 0.6315 (mmm) cc_final: 0.4712 (ptp) REVERT: D 473 MET cc_start: 0.7717 (mtt) cc_final: 0.7306 (mtt) REVERT: E 473 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: F 473 MET cc_start: 0.7721 (mtt) cc_final: 0.7310 (mtt) REVERT: G 421 MET cc_start: 0.8263 (mtt) cc_final: 0.7982 (mtt) REVERT: G 473 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7242 (mtt) REVERT: H 473 MET cc_start: 0.7698 (mtt) cc_final: 0.7302 (mtt) REVERT: I 385 MET cc_start: 0.6277 (mmm) cc_final: 0.4706 (ptp) REVERT: I 473 MET cc_start: 0.7674 (mtt) cc_final: 0.7269 (mtt) REVERT: J 385 MET cc_start: 0.6301 (mmm) cc_final: 0.4710 (ptp) REVERT: J 473 MET cc_start: 0.7715 (mtt) cc_final: 0.7306 (mtt) REVERT: K 473 MET cc_start: 0.7714 (mtt) cc_final: 0.7322 (mtt) REVERT: L 473 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7231 (mtt) REVERT: M 385 MET cc_start: 0.6359 (mmm) cc_final: 0.4792 (ptp) REVERT: M 473 MET cc_start: 0.7705 (mtt) cc_final: 0.7290 (mtt) REVERT: N 473 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7243 (mtt) REVERT: O 473 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7230 (mtt) REVERT: P 385 MET cc_start: 0.6358 (mmm) cc_final: 0.4794 (ptp) REVERT: P 473 MET cc_start: 0.7657 (mtt) cc_final: 0.7240 (mtt) REVERT: Q 473 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7216 (mtt) REVERT: R 385 MET cc_start: 0.6314 (mmm) cc_final: 0.4717 (ptp) REVERT: R 421 MET cc_start: 0.8480 (mtt) cc_final: 0.8067 (mtt) REVERT: R 473 MET cc_start: 0.7718 (mtt) cc_final: 0.7308 (mtt) REVERT: S 385 MET cc_start: 0.6312 (mmm) cc_final: 0.4700 (ptp) REVERT: S 473 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: T 473 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7223 (mtt) REVERT: V 385 MET cc_start: 0.6298 (mmm) cc_final: 0.4721 (ptp) REVERT: V 473 MET cc_start: 0.7724 (mtt) cc_final: 0.7312 (mtt) REVERT: W 385 MET cc_start: 0.6392 (mmm) cc_final: 0.4790 (ptp) REVERT: W 473 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7215 (mtt) REVERT: X 385 MET cc_start: 0.6299 (mmm) cc_final: 0.4719 (ptp) REVERT: X 473 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7219 (mtt) REVERT: Y 385 MET cc_start: 0.6312 (mmm) cc_final: 0.4715 (ptp) REVERT: Y 421 MET cc_start: 0.8482 (mtt) cc_final: 0.8067 (mtt) REVERT: Y 473 MET cc_start: 0.7718 (mtt) cc_final: 0.7307 (mtt) outliers start: 100 outliers final: 86 residues processed: 563 average time/residue: 0.5348 time to fit residues: 505.1529 Evaluate side-chains 561 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 463 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 503 ASN Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 442 GLN Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain J residue 503 ASN Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 442 GLN Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 442 GLN Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 442 GLN Chi-restraints excluded: chain M residue 503 ASN Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 503 ASN Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 442 GLN Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 442 GLN Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 410 ILE Chi-restraints excluded: chain V residue 442 GLN Chi-restraints excluded: chain V residue 503 ASN Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 410 ILE Chi-restraints excluded: chain W residue 442 GLN Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 442 GLN Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 0.0970 chunk 531 optimal weight: 10.0000 chunk 485 optimal weight: 0.9980 chunk 517 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 467 optimal weight: 2.9990 chunk 489 optimal weight: 9.9990 chunk 515 optimal weight: 4.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 46824 Z= 0.300 Angle : 0.505 4.448 63192 Z= 0.271 Chirality : 0.044 0.127 7296 Planarity : 0.005 0.044 8064 Dihedral : 3.742 12.228 6240 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.76 % Favored : 96.84 % Rotamer: Outliers : 2.63 % Allowed : 12.52 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.72 (0.11), residues: 5880 helix: 2.11 (0.11), residues: 2280 sheet: -0.50 (0.14), residues: 1152 loop : -0.56 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 583 HIS 0.003 0.001 HIS R 424 PHE 0.014 0.002 PHE D 560 TYR 0.004 0.001 TYR K 492 ARG 0.004 0.000 ARG O 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 471 time to evaluate : 5.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ILE cc_start: 0.6139 (OUTLIER) cc_final: 0.5790 (tp) REVERT: A 473 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7141 (mtt) REVERT: B 407 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5783 (tp) REVERT: B 473 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7128 (mtt) REVERT: C 407 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5782 (tp) REVERT: C 473 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7158 (mtt) REVERT: D 385 MET cc_start: 0.6352 (mmm) cc_final: 0.4689 (ptp) REVERT: D 473 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: E 407 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5781 (tp) REVERT: E 473 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (mtt) REVERT: F 407 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5772 (tp) REVERT: F 473 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7183 (mtt) REVERT: G 421 MET cc_start: 0.8372 (mtt) cc_final: 0.8020 (mtt) REVERT: G 473 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7128 (mtt) REVERT: H 473 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7154 (mtt) REVERT: I 385 MET cc_start: 0.6318 (mmm) cc_final: 0.4666 (ptp) REVERT: I 407 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5762 (tp) REVERT: I 473 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7180 (mtt) REVERT: J 385 MET cc_start: 0.6345 (mmm) cc_final: 0.4674 (ptp) REVERT: J 407 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5778 (tp) REVERT: J 473 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7177 (mtt) REVERT: K 407 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5768 (tp) REVERT: K 473 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: L 407 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5780 (tp) REVERT: L 473 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7142 (mtt) REVERT: M 385 MET cc_start: 0.6393 (mmm) cc_final: 0.4746 (ptp) REVERT: M 473 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7159 (mtt) REVERT: N 421 MET cc_start: 0.8241 (mtt) cc_final: 0.8003 (mtt) REVERT: N 473 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7130 (mtt) REVERT: O 407 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5774 (tp) REVERT: O 473 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7140 (mtt) REVERT: P 385 MET cc_start: 0.6396 (mmm) cc_final: 0.4749 (ptp) REVERT: P 473 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7158 (mtt) REVERT: Q 473 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7129 (mtt) REVERT: R 385 MET cc_start: 0.6355 (mmm) cc_final: 0.4702 (ptp) REVERT: R 421 MET cc_start: 0.8449 (mtt) cc_final: 0.8038 (mtt) REVERT: R 473 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7180 (mtt) REVERT: S 385 MET cc_start: 0.6356 (mmm) cc_final: 0.4687 (ptp) REVERT: S 407 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5774 (tp) REVERT: S 473 MET cc_start: 0.7583 (mtt) cc_final: 0.7210 (mtt) REVERT: T 421 MET cc_start: 0.8239 (mtt) cc_final: 0.8002 (mtt) REVERT: T 473 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7128 (mtt) REVERT: V 385 MET cc_start: 0.6336 (mmm) cc_final: 0.4685 (ptp) REVERT: V 473 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7185 (mtt) REVERT: W 385 MET cc_start: 0.6425 (mmm) cc_final: 0.4767 (ptp) REVERT: W 421 MET cc_start: 0.8282 (mtt) cc_final: 0.8061 (mtt) REVERT: W 473 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7206 (mtt) REVERT: X 385 MET cc_start: 0.6344 (mmm) cc_final: 0.4685 (ptp) REVERT: X 473 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7133 (mtt) REVERT: Y 385 MET cc_start: 0.6353 (mmm) cc_final: 0.4698 (ptp) REVERT: Y 421 MET cc_start: 0.8451 (mtt) cc_final: 0.8038 (mtt) REVERT: Y 473 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7179 (mtt) outliers start: 133 outliers final: 96 residues processed: 554 average time/residue: 0.5510 time to fit residues: 510.3450 Evaluate side-chains 595 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 465 time to evaluate : 5.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 503 ASN Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 442 GLN Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 503 ASN Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 442 GLN Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 503 ASN Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 407 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 442 GLN Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 407 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 442 GLN Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 442 GLN Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 503 ASN Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 442 GLN Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 503 ASN Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 473 MET Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 442 GLN Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 442 GLN Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 442 GLN Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 407 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 442 GLN Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 410 ILE Chi-restraints excluded: chain V residue 442 GLN Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 503 ASN Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 410 ILE Chi-restraints excluded: chain W residue 442 GLN Chi-restraints excluded: chain W residue 473 MET Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 442 GLN Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 9.9990 chunk 547 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 573 optimal weight: 0.9990 chunk 528 optimal weight: 6.9990 chunk 456 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 352 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 442 GLN C 442 GLN G 442 GLN I 442 GLN N 442 GLN P 442 GLN Q 442 GLN R 442 GLN T 442 GLN X 442 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 46824 Z= 0.210 Angle : 0.456 4.281 63192 Z= 0.244 Chirality : 0.042 0.127 7296 Planarity : 0.005 0.044 8064 Dihedral : 3.549 12.638 6240 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.18 % Favored : 97.41 % Rotamer: Outliers : 2.27 % Allowed : 13.11 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.96 (0.11), residues: 5880 helix: 2.35 (0.11), residues: 2280 sheet: -0.37 (0.14), residues: 1152 loop : -0.47 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 583 HIS 0.002 0.001 HIS T 559 PHE 0.013 0.002 PHE C 613 TYR 0.002 0.001 TYR E 492 ARG 0.004 0.000 ARG A 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11760 Ramachandran restraints generated. 5880 Oldfield, 0 Emsley, 5880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 479 time to evaluate : 5.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 385 MET cc_start: 0.4172 (ttp) cc_final: 0.3932 (ttp) REVERT: B 473 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7107 (mtt) REVERT: C 385 MET cc_start: 0.4110 (ttp) cc_final: 0.3872 (ttp) REVERT: C 407 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5745 (tp) REVERT: C 473 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7252 (mtt) REVERT: D 385 MET cc_start: 0.6356 (mmm) cc_final: 0.4679 (ptp) REVERT: D 407 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5662 (tp) REVERT: D 473 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7274 (mtt) REVERT: E 407 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5745 (tp) REVERT: E 473 MET cc_start: 0.7542 (mtt) cc_final: 0.7197 (mtt) REVERT: F 407 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5733 (tp) REVERT: F 473 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7280 (mtt) REVERT: G 421 MET cc_start: 0.8393 (mtt) cc_final: 0.7970 (mtt) REVERT: G 473 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7203 (mtt) REVERT: H 473 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7251 (mtt) REVERT: I 385 MET cc_start: 0.6387 (mmm) cc_final: 0.4693 (ptp) REVERT: I 407 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5682 (tp) REVERT: I 473 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: J 385 MET cc_start: 0.6345 (mmm) cc_final: 0.4682 (ptp) REVERT: J 407 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5738 (tp) REVERT: J 473 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: K 385 MET cc_start: 0.4044 (ttp) cc_final: 0.3799 (ttp) REVERT: K 407 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5730 (tp) REVERT: K 473 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7270 (mtt) REVERT: L 407 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.5740 (tp) REVERT: L 473 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7128 (mtt) REVERT: M 385 MET cc_start: 0.6468 (mmm) cc_final: 0.4774 (ptp) REVERT: M 421 MET cc_start: 0.8212 (mtt) cc_final: 0.7913 (mtt) REVERT: M 473 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7256 (mtt) REVERT: N 421 MET cc_start: 0.8240 (mtt) cc_final: 0.7920 (mtt) REVERT: N 473 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7205 (mtt) REVERT: P 385 MET cc_start: 0.6469 (mmm) cc_final: 0.4778 (ptp) REVERT: P 421 MET cc_start: 0.8213 (mtt) cc_final: 0.7916 (mtt) REVERT: P 473 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7252 (mtt) REVERT: Q 385 MET cc_start: 0.4166 (ttp) cc_final: 0.3951 (ttp) REVERT: Q 473 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7110 (mtt) REVERT: R 385 MET cc_start: 0.6352 (mmm) cc_final: 0.4686 (ptp) REVERT: R 421 MET cc_start: 0.8354 (mtt) cc_final: 0.7930 (mtt) REVERT: R 473 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7276 (mtt) REVERT: S 385 MET cc_start: 0.6352 (mmm) cc_final: 0.4638 (ptp) REVERT: S 407 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5737 (tp) REVERT: S 473 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7177 (mtt) REVERT: T 421 MET cc_start: 0.8238 (mtt) cc_final: 0.7918 (mtt) REVERT: T 473 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7183 (mtt) REVERT: V 385 MET cc_start: 0.6406 (mmm) cc_final: 0.4708 (ptp) REVERT: V 421 MET cc_start: 0.8229 (mtt) cc_final: 0.7918 (mtt) REVERT: V 473 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: W 385 MET cc_start: 0.6426 (mmm) cc_final: 0.4754 (ptp) REVERT: W 421 MET cc_start: 0.8275 (mtt) cc_final: 0.7957 (mtt) REVERT: W 473 MET cc_start: 0.7544 (mtt) cc_final: 0.7199 (mtt) REVERT: X 385 MET cc_start: 0.6414 (mmm) cc_final: 0.4720 (ptp) REVERT: X 473 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7113 (mtt) REVERT: Y 385 MET cc_start: 0.6351 (mmm) cc_final: 0.4683 (ptp) REVERT: Y 421 MET cc_start: 0.8354 (mtt) cc_final: 0.7928 (mtt) REVERT: Y 473 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7277 (mtt) outliers start: 115 outliers final: 86 residues processed: 550 average time/residue: 0.5464 time to fit residues: 502.0549 Evaluate side-chains 588 residues out of total 5064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 473 time to evaluate : 5.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 442 GLN Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 503 ASN Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 442 GLN Chi-restraints excluded: chain E residue 503 ASN Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 442 GLN Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 528 ILE Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 442 GLN Chi-restraints excluded: chain H residue 473 MET Chi-restraints excluded: chain H residue 528 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 442 GLN Chi-restraints excluded: chain I residue 473 MET Chi-restraints excluded: chain I residue 503 ASN Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 442 GLN Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain K residue 407 ILE Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 442 GLN Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain L residue 407 ILE Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 442 GLN Chi-restraints excluded: chain L residue 473 MET Chi-restraints excluded: chain L residue 503 ASN Chi-restraints excluded: chain L residue 528 ILE Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 442 GLN Chi-restraints excluded: chain M residue 473 MET Chi-restraints excluded: chain M residue 528 ILE Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 442 GLN Chi-restraints excluded: chain N residue 473 MET Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 503 ASN Chi-restraints excluded: chain O residue 528 ILE Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 442 GLN Chi-restraints excluded: chain P residue 473 MET Chi-restraints excluded: chain P residue 503 ASN Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain Q residue 410 ILE Chi-restraints excluded: chain Q residue 442 GLN Chi-restraints excluded: chain Q residue 473 MET Chi-restraints excluded: chain Q residue 503 ASN Chi-restraints excluded: chain Q residue 528 ILE Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 442 GLN Chi-restraints excluded: chain R residue 473 MET Chi-restraints excluded: chain R residue 503 ASN Chi-restraints excluded: chain R residue 528 ILE Chi-restraints excluded: chain S residue 407 ILE Chi-restraints excluded: chain S residue 410 ILE Chi-restraints excluded: chain S residue 442 GLN Chi-restraints excluded: chain S residue 473 MET Chi-restraints excluded: chain S residue 503 ASN Chi-restraints excluded: chain S residue 528 ILE Chi-restraints excluded: chain T residue 410 ILE Chi-restraints excluded: chain T residue 442 GLN Chi-restraints excluded: chain T residue 473 MET Chi-restraints excluded: chain T residue 503 ASN Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain V residue 410 ILE Chi-restraints excluded: chain V residue 442 GLN Chi-restraints excluded: chain V residue 473 MET Chi-restraints excluded: chain V residue 528 ILE Chi-restraints excluded: chain W residue 410 ILE Chi-restraints excluded: chain W residue 442 GLN Chi-restraints excluded: chain W residue 503 ASN Chi-restraints excluded: chain W residue 528 ILE Chi-restraints excluded: chain X residue 410 ILE Chi-restraints excluded: chain X residue 442 GLN Chi-restraints excluded: chain X residue 473 MET Chi-restraints excluded: chain X residue 503 ASN Chi-restraints excluded: chain X residue 528 ILE Chi-restraints excluded: chain Y residue 410 ILE Chi-restraints excluded: chain Y residue 473 MET Chi-restraints excluded: chain Y residue 503 ASN Chi-restraints excluded: chain Y residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 8.9990 chunk 486 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 421 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 457 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 469 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.219840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.169771 restraints weight = 44920.026| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.24 r_work: 0.3735 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 46824 Z= 0.256 Angle : 0.479 4.357 63192 Z= 0.257 Chirality : 0.043 0.131 7296 Planarity : 0.005 0.044 8064 Dihedral : 3.636 12.861 6240 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.59 % Favored : 97.01 % Rotamer: Outliers : 2.65 % Allowed : 13.39 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.88 (0.11), residues: 5880 helix: 2.29 (0.11), residues: 2280 sheet: -0.44 (0.14), residues: 1152 loop : -0.50 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 583 HIS 0.002 0.001 HIS J 424 PHE 0.013 0.002 PHE C 613 TYR 0.003 0.001 TYR B 492 ARG 0.004 0.000 ARG L 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9871.60 seconds wall clock time: 178 minutes 52.12 seconds (10732.12 seconds total)