Starting phenix.real_space_refine on Sat Feb 17 17:17:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytc_34085/02_2024/7ytc_34085.pdb" } resolution = 3.39 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= 0.006 sd= 0.049 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 95 5.16 5 C 12167 2.51 5 N 3276 2.21 5 O 3790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C GLU 508": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "E PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E GLU 526": "OE1" <-> "OE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 532": "OE1" <-> "OE2" Residue "E ASP 553": "OD1" <-> "OD2" Residue "E TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "G GLU 388": "OE1" <-> "OE2" Residue "G PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 491": "NH1" <-> "NH2" Residue "G TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 526": "OE1" <-> "OE2" Residue "G ASP 553": "OD1" <-> "OD2" Residue "G TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 527": "OE1" <-> "OE2" Residue "H GLU 549": "OE1" <-> "OE2" Residue "H TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 104": "OD1" <-> "OD2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 410": "OE1" <-> "OE2" Residue "K PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 483": "OD1" <-> "OD2" Residue "K TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 526": "OE1" <-> "OE2" Residue "K ASP 553": "OD1" <-> "OD2" Residue "L PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ARG 451": "NH1" <-> "NH2" Residue "L GLU 462": "OE1" <-> "OE2" Residue "L GLU 498": "OE1" <-> "OE2" Residue "L TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 508": "OE1" <-> "OE2" Residue "L TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 526": "OE1" <-> "OE2" Residue "L TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 41": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19328 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1780 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1769 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain: "C" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1742 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 825 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain breaks: 1 Chain: "K" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1749 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 206} Chain: "L" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1773 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.62, per 1000 atoms: 0.50 Number of scatterers: 19328 At special positions: 0 Unit cell: (116.748, 189.612, 163.116, 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 95 16.00 O 3790 8.00 N 3276 7.00 C 12167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.04 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.05 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.05 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.04 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.04 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.04 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.04 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.03 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=2.03 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.04 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.01 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 426 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19284 O5 NAG H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG E 601 " - " ASN E 563 " " NAG F 601 " - " ASN F 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG J 201 " - " ASN J 48 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " Time building additional restraints: 6.49 Conformation dependent library (CDL) restraints added in 3.4 seconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 60 sheets defined 9.4% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 461 through 465 removed outlier: 3.587A pdb=" N ASN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.957A pdb=" N THR A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.606A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 4.058A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 4.015A pdb=" N GLY B 557 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.718A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 467 removed outlier: 3.550A pdb=" N ARG C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.799A pdb=" N THR C 530 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 removed outlier: 4.267A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 460 through 467 removed outlier: 4.113A pdb=" N LEU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 529 removed outlier: 3.861A pdb=" N TRP D 528 " --> pdb=" O SER D 524 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 529 " --> pdb=" O GLU D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 529' Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 524 through 531 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 419 removed outlier: 4.078A pdb=" N TRP F 418 " --> pdb=" O CYS F 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN F 419 " --> pdb=" O GLU F 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 414 through 419' Processing helix chain 'F' and resid 524 through 529 removed outlier: 3.608A pdb=" N TRP F 528 " --> pdb=" O SER F 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 359 removed outlier: 3.817A pdb=" N LEU G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 524 through 530 removed outlier: 4.023A pdb=" N TRP G 528 " --> pdb=" O SER G 524 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN G 529 " --> pdb=" O GLU G 525 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 524 through 530' Processing helix chain 'G' and resid 553 through 557 removed outlier: 3.954A pdb=" N GLY G 557 " --> pdb=" O LYS G 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 361 Processing helix chain 'H' and resid 415 through 419 removed outlier: 4.192A pdb=" N ASN H 419 " --> pdb=" O ASP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 530 removed outlier: 3.514A pdb=" N THR H 530 " --> pdb=" O GLU H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 557 removed outlier: 3.590A pdb=" N THR H 556 " --> pdb=" O ASP H 553 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY H 557 " --> pdb=" O LYS H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 553 through 557' Processing helix chain 'K' and resid 414 through 419 removed outlier: 4.134A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 414 through 419' Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 525 through 529 removed outlier: 3.852A pdb=" N ASN K 529 " --> pdb=" O GLU K 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 525 through 529' Processing helix chain 'L' and resid 353 through 358 removed outlier: 3.673A pdb=" N PHE L 358 " --> pdb=" O PHE L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 420 removed outlier: 4.013A pdb=" N ASN L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 525 through 530 Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 3.537A pdb=" N ALA A 407 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 371 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE A 405 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 383 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.586A pdb=" N PHE A 485 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 562 through 563 removed outlier: 6.791A pdb=" N TYR A 562 " --> pdb=" O ASN B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.975A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 350 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 454 through 457 removed outlier: 6.091A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AB3, first strand: chain 'C' and resid 346 through 350 Processing sheet with id=AB4, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AB5, first strand: chain 'C' and resid 456 through 457 Processing sheet with id=AB6, first strand: chain 'C' and resid 477 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB8, first strand: chain 'D' and resid 346 through 350 removed outlier: 4.120A pdb=" N ALA D 407 " --> pdb=" O VAL D 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.706A pdb=" N THR D 425 " --> pdb=" O THR D 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.480A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 493 through 494 Processing sheet with id=AC4, first strand: chain 'D' and resid 565 through 567 removed outlier: 7.240A pdb=" N LEU D 566 " --> pdb=" O VAL E 567 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 346 through 350 Processing sheet with id=AC6, first strand: chain 'E' and resid 379 through 383 removed outlier: 3.656A pdb=" N LEU E 437 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 453 through 457 removed outlier: 3.505A pdb=" N THR E 477 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 473 " --> pdb=" O LEU E 457 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 493 through 494 removed outlier: 3.736A pdb=" N GLN E 493 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AD2, first strand: chain 'F' and resid 379 through 383 Processing sheet with id=AD3, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 453 through 457 removed outlier: 4.132A pdb=" N THR F 477 " --> pdb=" O ASP F 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL F 476 " --> pdb=" O ALA F 517 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD6, first strand: chain 'F' and resid 565 through 567 Processing sheet with id=AD7, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA G 407 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE G 405 " --> pdb=" O ASP G 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 347 through 350 removed outlier: 3.937A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 379 through 383 Processing sheet with id=AE1, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE2, first strand: chain 'G' and resid 453 through 457 Processing sheet with id=AE3, first strand: chain 'G' and resid 493 through 494 removed outlier: 3.816A pdb=" N GLN G 493 " --> pdb=" O GLN G 490 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN G 490 " --> pdb=" O GLN G 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 346 through 350 Processing sheet with id=AE5, first strand: chain 'H' and resid 379 through 383 removed outlier: 3.742A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE H 424 " --> pdb=" O ILE H 441 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.907A pdb=" N THR H 477 " --> pdb=" O ASP H 453 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AE9, first strand: chain 'H' and resid 566 through 567 Processing sheet with id=AF1, first strand: chain 'J' and resid 21 through 22 removed outlier: 4.432A pdb=" N ILE J 32 " --> pdb=" O ILE J 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AF3, first strand: chain 'J' and resid 110 through 113 removed outlier: 3.688A pdb=" N ALA J 111 " --> pdb=" O THR J 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AF5, first strand: chain 'K' and resid 379 through 384 Processing sheet with id=AF6, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.660A pdb=" N THR K 477 " --> pdb=" O ASP K 453 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AF8, first strand: chain 'K' and resid 506 through 507 Processing sheet with id=AF9, first strand: chain 'K' and resid 561 through 562 removed outlier: 6.346A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 346 through 350 Processing sheet with id=AG2, first strand: chain 'L' and resid 380 through 383 removed outlier: 4.090A pdb=" N PHE L 424 " --> pdb=" O ILE L 441 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 441 " --> pdb=" O PHE L 424 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN L 439 " --> pdb=" O CYS L 426 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 454 through 457 removed outlier: 4.038A pdb=" N GLY L 478 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR L 515 " --> pdb=" O GLY L 478 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 493 through 495 removed outlier: 4.278A pdb=" N TRP L 488 " --> pdb=" O LEU L 495 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 539 " --> pdb=" O PHE L 485 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 33 through 37 removed outlier: 4.203A pdb=" N LEU R 86 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR R 81 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 58 through 62 removed outlier: 5.362A pdb=" N THR R 60 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG R 50 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR R 47 " --> pdb=" O GLY R 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL R 101 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN R 116 " --> pdb=" O CYS R 104 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1494 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: 5.98 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3154 1.25 - 1.40: 4597 1.40 - 1.54: 11748 1.54 - 1.68: 174 1.68 - 1.83: 129 Bond restraints: 19802 Sorted by residual: bond pdb=" CA ASN H 563 " pdb=" C ASN H 563 " ideal model delta sigma weight residual 1.524 1.389 0.134 1.30e-02 5.92e+03 1.07e+02 bond pdb=" C ASN H 563 " pdb=" O ASN H 563 " ideal model delta sigma weight residual 1.234 1.111 0.123 1.22e-02 6.72e+03 1.02e+02 bond pdb=" CA ALA B 517 " pdb=" C ALA B 517 " ideal model delta sigma weight residual 1.520 1.406 0.114 1.20e-02 6.94e+03 9.05e+01 bond pdb=" C ILE J 39 " pdb=" O ILE J 39 " ideal model delta sigma weight residual 1.238 1.137 0.100 1.06e-02 8.90e+03 8.98e+01 bond pdb=" C VAL C 564 " pdb=" O VAL C 564 " ideal model delta sigma weight residual 1.237 1.146 0.091 9.80e-03 1.04e+04 8.59e+01 ... (remaining 19797 not shown) Histogram of bond angle deviations from ideal: 92.25 - 102.44: 112 102.44 - 112.62: 11273 112.62 - 122.81: 13151 122.81 - 132.99: 2509 132.99 - 143.18: 48 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N THR B 533 " pdb=" CA THR B 533 " pdb=" C THR B 533 " ideal model delta sigma weight residual 111.28 133.25 -21.97 1.09e+00 8.42e-01 4.06e+02 angle pdb=" N THR K 533 " pdb=" CA THR K 533 " pdb=" C THR K 533 " ideal model delta sigma weight residual 111.28 127.21 -15.93 1.09e+00 8.42e-01 2.14e+02 angle pdb=" C SER L 496 " pdb=" N PRO L 497 " pdb=" CA PRO L 497 " ideal model delta sigma weight residual 119.87 134.35 -14.48 1.04e+00 9.25e-01 1.94e+02 angle pdb=" C LYS F 558 " pdb=" N PRO F 559 " pdb=" CA PRO F 559 " ideal model delta sigma weight residual 119.05 134.25 -15.20 1.11e+00 8.12e-01 1.88e+02 angle pdb=" N PRO B 452 " pdb=" CA PRO B 452 " pdb=" C PRO B 452 " ideal model delta sigma weight residual 113.84 130.83 -16.99 1.30e+00 5.92e-01 1.71e+02 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.57: 11027 21.57 - 43.15: 902 43.15 - 64.72: 217 64.72 - 86.29: 40 86.29 - 107.87: 10 Dihedral angle restraints: 12196 sinusoidal: 4949 harmonic: 7247 Sorted by residual: dihedral pdb=" C THR F 560 " pdb=" N THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual -122.00 -151.55 29.55 0 2.50e+00 1.60e-01 1.40e+02 dihedral pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CA THR F 560 " pdb=" CB THR F 560 " ideal model delta harmonic sigma weight residual 123.40 151.69 -28.29 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C ASN R 85 " pdb=" N ASN R 85 " pdb=" CA ASN R 85 " pdb=" CB ASN R 85 " ideal model delta harmonic sigma weight residual -122.60 -146.78 24.18 0 2.50e+00 1.60e-01 9.36e+01 ... (remaining 12193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 3161 0.270 - 0.540: 51 0.540 - 0.809: 7 0.809 - 1.079: 1 1.079 - 1.349: 1 Chirality restraints: 3221 Sorted by residual: chirality pdb=" CA THR F 560 " pdb=" N THR F 560 " pdb=" C THR F 560 " pdb=" CB THR F 560 " both_signs ideal model delta sigma weight residual False 2.53 1.18 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA ASN R 85 " pdb=" N ASN R 85 " pdb=" C ASN R 85 " pdb=" CB ASN R 85 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA THR B 533 " pdb=" N THR B 533 " pdb=" C THR B 533 " pdb=" CB THR B 533 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3218 not shown) Planarity restraints: 3467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 558 " -0.101 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO K 559 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO K 559 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO K 559 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 562 " 0.030 2.00e-02 2.50e+03 5.98e-02 3.57e+01 pdb=" C TYR C 562 " -0.103 2.00e-02 2.50e+03 pdb=" O TYR C 562 " 0.038 2.00e-02 2.50e+03 pdb=" N ASN C 563 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 488 " 0.027 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" C TRP B 488 " -0.095 2.00e-02 2.50e+03 pdb=" O TRP B 488 " 0.036 2.00e-02 2.50e+03 pdb=" N MET B 489 " 0.033 2.00e-02 2.50e+03 ... (remaining 3464 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 28 1.95 - 2.68: 1065 2.68 - 3.42: 25865 3.42 - 4.16: 44293 4.16 - 4.90: 76988 Nonbonded interactions: 148239 Sorted by model distance: nonbonded pdb=" NH1 ARG C 384 " pdb=" O ALA C 389 " model vdw 1.208 2.520 nonbonded pdb=" O ARG L 491 " pdb=" NE2 GLN L 493 " model vdw 1.411 2.520 nonbonded pdb=" OD2 ASP E 453 " pdb=" CE2 TYR E 455 " model vdw 1.433 3.340 nonbonded pdb=" OD2 ASP E 453 " pdb=" CZ TYR E 455 " model vdw 1.501 3.260 nonbonded pdb=" OD1 ASN C 386 " pdb=" CG GLU C 388 " model vdw 1.537 3.440 ... (remaining 148234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'B' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'C' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 568 o \ r resid 601)) selection = (chain 'D' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'E' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'F' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'G' and (resid 345 through 444 or resid 449 through 512 or (resid 513 and \ (name N or name CA or name C )) or resid 514 through 568 or resid 601)) selection = (chain 'H' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'K' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 444 or resid 449 through 512 o \ r (resid 513 and (name N or name CA or name C )) or resid 514 through 568 or res \ id 601)) selection = (chain 'L' and ((resid 345 and (name N or name CA or name C or name CB or name C \ G1 or name CG2 or name CD1)) or resid 346 through 512 or (resid 513 and (name N \ or name CA or name C )) or resid 514 through 568 or resid 601)) } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.170 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 48.430 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.011 0.144 19802 Z= 0.698 Angle : 1.322 21.968 27093 Z= 0.828 Chirality : 0.087 1.349 3221 Planarity : 0.008 0.151 3456 Dihedral : 16.748 107.868 7388 Min Nonbonded Distance : 1.208 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.02 % Favored : 90.44 % Rotamer: Outliers : 8.45 % Allowed : 3.41 % Favored : 88.15 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2438 helix: -2.45 (0.36), residues: 151 sheet: -0.93 (0.17), residues: 897 loop : -2.01 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 528 HIS 0.016 0.001 HIS D 450 PHE 0.079 0.002 PHE G 479 TYR 0.047 0.003 TYR J 101 ARG 0.015 0.001 ARG F 451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 312 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 364 LYS cc_start: 0.6689 (pttt) cc_final: 0.6292 (ptpt) REVERT: B 415 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6292 (mt-10) REVERT: C 416 ASP cc_start: 0.9239 (m-30) cc_final: 0.9034 (p0) REVERT: C 566 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8665 (pp) REVERT: D 424 PHE cc_start: 0.8515 (m-80) cc_final: 0.8263 (m-80) REVERT: D 534 TYR cc_start: 0.7701 (m-80) cc_final: 0.7359 (m-10) REVERT: E 500 TYR cc_start: 0.8833 (p90) cc_final: 0.8493 (p90) REVERT: E 503 SER cc_start: 0.8521 (t) cc_final: 0.8291 (m) REVERT: F 424 PHE cc_start: 0.7438 (m-80) cc_final: 0.7179 (m-80) REVERT: F 449 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7482 (pp) REVERT: F 451 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8147 (mtm-85) REVERT: G 364 LYS cc_start: 0.8110 (tptt) cc_final: 0.7738 (tppt) REVERT: G 490 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6360 (tp40) REVERT: H 566 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8630 (mp) REVERT: J 9 ASP cc_start: 0.7874 (t70) cc_final: 0.7461 (t70) REVERT: K 463 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7800 (tm-30) REVERT: K 530 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.5850 (t) REVERT: K 554 LYS cc_start: 0.8667 (tttt) cc_final: 0.8341 (tttm) REVERT: L 450 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.5654 (m90) REVERT: L 451 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: L 486 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8441 (t) REVERT: L 500 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.6152 (p90) REVERT: L 514 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.4898 (ptp90) REVERT: L 570 ASP cc_start: 0.7952 (t0) cc_final: 0.7696 (t0) REVERT: R 50 ARG cc_start: 0.7388 (ttt180) cc_final: 0.7006 (ttp80) REVERT: R 109 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7839 (t0) outliers start: 186 outliers final: 97 residues processed: 464 average time/residue: 0.3689 time to fit residues: 243.8147 Evaluate side-chains 360 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 250 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 450 HIS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 PRO Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 451 ARG Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 560 THR Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain E residue 562 TYR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 450 HIS Chi-restraints excluded: chain F residue 451 ARG Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 449 LEU Chi-restraints excluded: chain G residue 485 PHE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain H residue 443 ARG Chi-restraints excluded: chain H residue 449 LEU Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 551 THR Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain H residue 563 ASN Chi-restraints excluded: chain H residue 566 LEU Chi-restraints excluded: chain H residue 567 VAL Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 443 ARG Chi-restraints excluded: chain K residue 450 HIS Chi-restraints excluded: chain K residue 451 ARG Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 516 PHE Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 529 ASN Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain K residue 555 SER Chi-restraints excluded: chain K residue 556 THR Chi-restraints excluded: chain L residue 443 ARG Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 484 VAL Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 496 SER Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 500 TYR Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain L residue 516 PHE Chi-restraints excluded: chain L residue 521 LEU Chi-restraints excluded: chain L residue 523 VAL Chi-restraints excluded: chain L residue 571 THR Chi-restraints excluded: chain R residue 28 GLU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 87 PHE Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 97 SER Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 109 ASN Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 ASN Chi-restraints excluded: chain R residue 123 HIS Chi-restraints excluded: chain R residue 124 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 73 optimal weight: 40.0000 chunk 114 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 218 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 450 HIS F 450 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19802 Z= 0.254 Angle : 0.694 13.715 27093 Z= 0.353 Chirality : 0.050 0.422 3221 Planarity : 0.006 0.083 3456 Dihedral : 10.860 87.820 3106 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.41 % Favored : 91.55 % Rotamer: Outliers : 4.86 % Allowed : 11.17 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2438 helix: -2.36 (0.32), residues: 166 sheet: -0.82 (0.17), residues: 899 loop : -2.04 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 382 HIS 0.008 0.001 HIS L 518 PHE 0.025 0.002 PHE B 348 TYR 0.029 0.002 TYR C 534 ARG 0.006 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 278 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 415 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: B 445 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7940 (pptt) REVERT: B 489 MET cc_start: 0.8151 (mtt) cc_final: 0.7887 (mtt) REVERT: B 499 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8181 (mtmt) REVERT: B 510 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7939 (pp30) REVERT: C 423 ARG cc_start: 0.7990 (ptm-80) cc_final: 0.7760 (ptm-80) REVERT: D 424 PHE cc_start: 0.8529 (m-80) cc_final: 0.8286 (m-80) REVERT: D 489 MET cc_start: 0.7905 (mtm) cc_final: 0.7631 (mtt) REVERT: D 534 TYR cc_start: 0.7757 (m-80) cc_final: 0.7508 (m-10) REVERT: E 500 TYR cc_start: 0.8884 (p90) cc_final: 0.8663 (p90) REVERT: E 554 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7421 (tmtt) REVERT: F 449 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7804 (pp) REVERT: F 453 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7573 (p0) REVERT: G 423 ARG cc_start: 0.6703 (mmt-90) cc_final: 0.6405 (mmt-90) REVERT: G 443 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7951 (ptm-80) REVERT: H 562 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.6928 (p90) REVERT: J 106 ASN cc_start: 0.7724 (p0) cc_final: 0.7326 (m-40) REVERT: K 514 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6675 (mtm-85) REVERT: K 530 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6345 (t) REVERT: K 554 LYS cc_start: 0.8358 (tttt) cc_final: 0.7936 (tttm) REVERT: L 450 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5634 (m90) REVERT: L 451 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7811 (ttm170) REVERT: L 486 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8444 (t) REVERT: R 121 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6587 (t0) outliers start: 107 outliers final: 59 residues processed: 351 average time/residue: 0.3696 time to fit residues: 184.9547 Evaluate side-chains 313 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 240 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 499 LYS Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 514 ARG Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 530 THR Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 486 VAL Chi-restraints excluded: chain L residue 499 LYS Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 121 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 30.0000 chunk 182 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 chunk 236 optimal weight: 0.0370 chunk 195 optimal weight: 40.0000 chunk 217 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN B 439 GLN B 490 GLN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 HIS H 430 HIS K 465 ASN ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19802 Z= 0.191 Angle : 0.630 10.974 27093 Z= 0.315 Chirality : 0.047 0.382 3221 Planarity : 0.005 0.066 3456 Dihedral : 8.786 69.381 2984 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.29 % Favored : 91.63 % Rotamer: Outliers : 4.04 % Allowed : 15.12 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.16), residues: 2438 helix: -2.13 (0.35), residues: 166 sheet: -0.58 (0.17), residues: 887 loop : -1.95 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 418 HIS 0.003 0.001 HIS C 393 PHE 0.019 0.001 PHE B 348 TYR 0.019 0.001 TYR K 534 ARG 0.005 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 265 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8280 (pptt) REVERT: B 489 MET cc_start: 0.8016 (mtt) cc_final: 0.7748 (mtt) REVERT: D 489 MET cc_start: 0.7959 (mtm) cc_final: 0.7576 (mtt) REVERT: E 440 THR cc_start: 0.5570 (OUTLIER) cc_final: 0.4949 (p) REVERT: E 449 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8417 (mm) REVERT: E 554 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7523 (tmtt) REVERT: F 449 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7797 (pp) REVERT: F 453 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7364 (p0) REVERT: G 364 LYS cc_start: 0.8128 (tptt) cc_final: 0.7746 (tppt) REVERT: G 443 ARG cc_start: 0.8209 (ptm-80) cc_final: 0.7692 (ptm160) REVERT: J 106 ASN cc_start: 0.7830 (p0) cc_final: 0.7473 (m-40) REVERT: K 416 ASP cc_start: 0.7421 (p0) cc_final: 0.7166 (p0) REVERT: K 418 TRP cc_start: 0.6169 (OUTLIER) cc_final: 0.5051 (m-90) REVERT: L 450 HIS cc_start: 0.5952 (OUTLIER) cc_final: 0.5687 (m90) REVERT: L 451 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: L 514 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.4527 (ptp90) outliers start: 89 outliers final: 59 residues processed: 325 average time/residue: 0.3641 time to fit residues: 170.8107 Evaluate side-chains 311 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain F residue 561 LEU Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 393 HIS Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 514 ARG Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 30.0000 chunk 164 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN B 490 GLN B 510 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19802 Z= 0.331 Angle : 0.671 12.451 27093 Z= 0.339 Chirality : 0.049 0.398 3221 Planarity : 0.005 0.065 3456 Dihedral : 7.890 64.124 2949 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer: Outliers : 5.00 % Allowed : 16.58 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.16), residues: 2438 helix: -2.01 (0.35), residues: 164 sheet: -0.61 (0.17), residues: 877 loop : -1.99 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 382 HIS 0.005 0.001 HIS H 518 PHE 0.020 0.002 PHE L 516 TYR 0.018 0.002 TYR K 534 ARG 0.008 0.001 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 245 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9207 (OUTLIER) cc_final: 0.8916 (m) REVERT: B 445 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8224 (pptt) REVERT: B 489 MET cc_start: 0.8334 (mtt) cc_final: 0.8089 (mtt) REVERT: B 491 ARG cc_start: 0.6305 (OUTLIER) cc_final: 0.5882 (mpt-90) REVERT: C 443 ARG cc_start: 0.5594 (ttp80) cc_final: 0.5372 (ptm160) REVERT: D 453 ASP cc_start: 0.7903 (m-30) cc_final: 0.7684 (m-30) REVERT: D 534 TYR cc_start: 0.7914 (m-10) cc_final: 0.7696 (m-80) REVERT: E 449 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8322 (mm) REVERT: E 554 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7479 (tmtt) REVERT: F 449 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7884 (pp) REVERT: F 453 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7339 (p0) REVERT: G 364 LYS cc_start: 0.8213 (tptt) cc_final: 0.7949 (tppt) REVERT: J 9 ASP cc_start: 0.8166 (t70) cc_final: 0.7935 (t0) REVERT: K 418 TRP cc_start: 0.6055 (OUTLIER) cc_final: 0.3584 (t-100) REVERT: K 463 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7519 (tm-30) REVERT: L 450 HIS cc_start: 0.5900 (OUTLIER) cc_final: 0.5591 (m90) REVERT: L 451 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7805 (ttm170) REVERT: L 561 LEU cc_start: 0.8685 (tt) cc_final: 0.8416 (pp) REVERT: R 90 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7851 (tm-30) outliers start: 110 outliers final: 75 residues processed: 323 average time/residue: 0.3669 time to fit residues: 169.7645 Evaluate side-chains 309 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 225 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 495 LEU Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 118 optimal weight: 7.9990 chunk 209 optimal weight: 40.0000 chunk 58 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 529 ASN D 487 GLN E 545 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS G 545 ASN ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19802 Z= 0.199 Angle : 0.609 10.602 27093 Z= 0.304 Chirality : 0.047 0.367 3221 Planarity : 0.005 0.061 3456 Dihedral : 7.436 59.370 2942 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.12 % Favored : 91.80 % Rotamer: Outliers : 4.45 % Allowed : 17.94 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -1.95 (0.17), residues: 2438 helix: -1.80 (0.36), residues: 163 sheet: -0.47 (0.17), residues: 882 loop : -1.82 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 382 HIS 0.004 0.001 HIS B 518 PHE 0.018 0.001 PHE L 516 TYR 0.017 0.001 TYR K 534 ARG 0.005 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 250 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8179 (m-80) cc_final: 0.7815 (m-80) REVERT: B 489 MET cc_start: 0.8239 (mtt) cc_final: 0.7976 (mtt) REVERT: B 491 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5813 (mpt-90) REVERT: B 510 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7857 (pp30) REVERT: C 391 LYS cc_start: 0.7653 (tmtt) cc_final: 0.6687 (ttmm) REVERT: D 534 TYR cc_start: 0.7852 (m-10) cc_final: 0.7608 (m-80) REVERT: E 433 LEU cc_start: 0.3158 (OUTLIER) cc_final: 0.2822 (mt) REVERT: E 449 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (mm) REVERT: E 500 TYR cc_start: 0.8866 (p90) cc_final: 0.8619 (p90) REVERT: E 554 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7362 (tptp) REVERT: F 391 LYS cc_start: 0.6267 (tptt) cc_final: 0.6044 (tptm) REVERT: F 449 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7861 (pp) REVERT: F 453 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7212 (p0) REVERT: G 364 LYS cc_start: 0.8224 (tptt) cc_final: 0.8008 (tptt) REVERT: H 380 ILE cc_start: 0.1342 (mm) cc_final: 0.0990 (tt) REVERT: H 473 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8735 (p) REVERT: K 418 TRP cc_start: 0.6150 (OUTLIER) cc_final: 0.3512 (t-100) REVERT: K 463 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7421 (tm-30) REVERT: L 450 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.5648 (m90) REVERT: L 451 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: L 452 PRO cc_start: 0.7354 (Cg_endo) cc_final: 0.7060 (Cg_exo) REVERT: R 90 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 98 outliers final: 71 residues processed: 315 average time/residue: 0.3878 time to fit residues: 178.8060 Evaluate side-chains 317 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 236 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 445 LYS Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.9980 chunk 209 optimal weight: 30.0000 chunk 46 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 193 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN E 487 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 19802 Z= 0.418 Angle : 0.698 13.108 27093 Z= 0.354 Chirality : 0.051 0.419 3221 Planarity : 0.005 0.061 3456 Dihedral : 7.490 59.684 2934 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.89 % Favored : 90.03 % Rotamer: Outliers : 5.27 % Allowed : 18.12 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2438 helix: -1.85 (0.35), residues: 176 sheet: -0.65 (0.17), residues: 900 loop : -1.96 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 382 HIS 0.006 0.001 HIS H 518 PHE 0.027 0.002 PHE L 479 TYR 0.016 0.002 TYR L 534 ARG 0.006 0.001 ARG J 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 235 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9203 (OUTLIER) cc_final: 0.8918 (m) REVERT: B 489 MET cc_start: 0.8375 (mtt) cc_final: 0.8145 (mtt) REVERT: B 491 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5765 (mpt-90) REVERT: B 510 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7885 (pp30) REVERT: C 391 LYS cc_start: 0.7646 (tmtt) cc_final: 0.6686 (ttmm) REVERT: D 353 SER cc_start: 0.7250 (t) cc_final: 0.7015 (p) REVERT: D 439 GLN cc_start: 0.5047 (tp40) cc_final: 0.4555 (tm-30) REVERT: D 453 ASP cc_start: 0.7916 (m-30) cc_final: 0.7706 (m-30) REVERT: E 449 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8336 (mm) REVERT: F 449 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7942 (pp) REVERT: F 453 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7377 (p0) REVERT: G 364 LYS cc_start: 0.8252 (tptt) cc_final: 0.7506 (tppt) REVERT: H 380 ILE cc_start: 0.1294 (mm) cc_final: 0.0960 (tt) REVERT: K 418 TRP cc_start: 0.6044 (OUTLIER) cc_final: 0.3226 (t-100) REVERT: L 450 HIS cc_start: 0.5995 (OUTLIER) cc_final: 0.5605 (m90) REVERT: L 451 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7989 (ttm170) REVERT: R 90 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7861 (tm-30) outliers start: 116 outliers final: 85 residues processed: 315 average time/residue: 0.3437 time to fit residues: 157.5879 Evaluate side-chains 315 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 221 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 553 ASP Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 461 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 548 THR Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 232 optimal weight: 40.0000 chunk 145 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 529 ASN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19802 Z= 0.204 Angle : 0.616 11.245 27093 Z= 0.306 Chirality : 0.047 0.360 3221 Planarity : 0.005 0.061 3456 Dihedral : 6.966 59.680 2927 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 4.90 % Allowed : 19.16 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -1.88 (0.17), residues: 2438 helix: -1.59 (0.36), residues: 175 sheet: -0.47 (0.17), residues: 890 loop : -1.77 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 382 HIS 0.003 0.001 HIS G 430 PHE 0.024 0.001 PHE L 479 TYR 0.015 0.001 TYR K 534 ARG 0.006 0.000 ARG C 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 241 time to evaluate : 2.227 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8174 (m-80) cc_final: 0.7917 (m-80) REVERT: A 537 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8890 (m) REVERT: B 489 MET cc_start: 0.8246 (mtt) cc_final: 0.7984 (mtt) REVERT: B 491 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5704 (mpt-90) REVERT: B 510 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7802 (pp30) REVERT: D 498 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: E 449 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8350 (mm) REVERT: E 554 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7330 (tptp) REVERT: F 449 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7963 (pp) REVERT: F 453 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7202 (p0) REVERT: G 364 LYS cc_start: 0.8198 (tptt) cc_final: 0.7438 (tppt) REVERT: H 380 ILE cc_start: 0.1207 (mm) cc_final: 0.0850 (tt) REVERT: K 418 TRP cc_start: 0.5953 (OUTLIER) cc_final: 0.3046 (t-100) REVERT: K 463 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7374 (tm-30) REVERT: L 450 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5730 (m90) REVERT: L 451 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: R 90 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 108 outliers final: 81 residues processed: 313 average time/residue: 0.3537 time to fit residues: 162.6278 Evaluate side-chains 319 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 228 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 506 MET Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 498 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 158 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN K 490 GLN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 19802 Z= 0.455 Angle : 0.716 13.397 27093 Z= 0.363 Chirality : 0.051 0.433 3221 Planarity : 0.006 0.061 3456 Dihedral : 7.244 58.883 2922 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.42 % Favored : 89.50 % Rotamer: Outliers : 5.31 % Allowed : 19.26 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.17), residues: 2438 helix: -1.63 (0.36), residues: 175 sheet: -0.66 (0.17), residues: 890 loop : -1.98 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 382 HIS 0.007 0.001 HIS H 518 PHE 0.026 0.002 PHE G 479 TYR 0.018 0.002 TYR D 534 ARG 0.008 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 220 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8926 (m) REVERT: B 489 MET cc_start: 0.8422 (mtt) cc_final: 0.8179 (mtt) REVERT: B 491 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5763 (mpt-90) REVERT: B 510 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7973 (pp30) REVERT: C 391 LYS cc_start: 0.7608 (tmtt) cc_final: 0.6678 (ttmm) REVERT: C 489 MET cc_start: 0.8632 (mtt) cc_final: 0.8321 (mtt) REVERT: D 353 SER cc_start: 0.7275 (t) cc_final: 0.7013 (p) REVERT: D 414 CYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5290 (m) REVERT: D 453 ASP cc_start: 0.7915 (m-30) cc_final: 0.7709 (m-30) REVERT: E 449 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8396 (mm) REVERT: F 449 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7956 (pp) REVERT: F 453 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7382 (p0) REVERT: F 461 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7458 (mtt180) REVERT: G 364 LYS cc_start: 0.8181 (tptt) cc_final: 0.7891 (tptt) REVERT: G 443 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7305 (ptm160) REVERT: H 380 ILE cc_start: 0.1228 (mm) cc_final: 0.0897 (tt) REVERT: K 418 TRP cc_start: 0.5978 (OUTLIER) cc_final: 0.3041 (t-100) REVERT: L 450 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5649 (m90) REVERT: L 451 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7979 (ttm170) REVERT: L 570 ASP cc_start: 0.7705 (t0) cc_final: 0.7462 (t0) REVERT: R 90 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7837 (tm-30) outliers start: 117 outliers final: 92 residues processed: 303 average time/residue: 0.3528 time to fit residues: 155.7731 Evaluate side-chains 315 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 213 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 418 TRP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 419 ASN Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 461 ARG Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 489 MET Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain G residue 545 ASN Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 142 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 529 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 GLN E 493 GLN ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19802 Z= 0.302 Angle : 0.659 12.760 27093 Z= 0.330 Chirality : 0.048 0.385 3221 Planarity : 0.005 0.057 3456 Dihedral : 7.013 58.866 2918 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 4.63 % Allowed : 20.48 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2438 helix: -1.65 (0.36), residues: 175 sheet: -0.62 (0.17), residues: 893 loop : -1.86 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 382 HIS 0.004 0.001 HIS H 518 PHE 0.026 0.002 PHE L 479 TYR 0.017 0.001 TYR D 534 ARG 0.015 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 228 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8906 (m) REVERT: B 489 MET cc_start: 0.8383 (mtt) cc_final: 0.8094 (mtt) REVERT: B 510 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7955 (pp30) REVERT: C 391 LYS cc_start: 0.7606 (tmtt) cc_final: 0.6634 (ttmm) REVERT: D 414 CYS cc_start: 0.5584 (OUTLIER) cc_final: 0.5278 (m) REVERT: D 453 ASP cc_start: 0.7910 (m-30) cc_final: 0.7695 (m-30) REVERT: E 449 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8379 (mm) REVERT: F 449 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8002 (pp) REVERT: F 453 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7315 (p0) REVERT: F 461 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7443 (mtt180) REVERT: G 364 LYS cc_start: 0.8073 (tptt) cc_final: 0.7656 (tppt) REVERT: G 443 ARG cc_start: 0.8427 (ptm160) cc_final: 0.8087 (ptm160) REVERT: H 380 ILE cc_start: 0.1141 (mm) cc_final: 0.0702 (tt) REVERT: H 534 TYR cc_start: 0.8773 (m-80) cc_final: 0.8158 (m-80) REVERT: K 418 TRP cc_start: 0.5988 (OUTLIER) cc_final: 0.2989 (t-100) REVERT: K 467 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7772 (tpp80) REVERT: L 450 HIS cc_start: 0.6061 (OUTLIER) cc_final: 0.5679 (m90) REVERT: L 451 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8150 (ptm160) REVERT: R 90 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7836 (tm-30) outliers start: 102 outliers final: 83 residues processed: 300 average time/residue: 0.3542 time to fit residues: 154.2466 Evaluate side-chains 313 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 221 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 220 optimal weight: 0.0010 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN B 529 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** K 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19802 Z= 0.242 Angle : 0.637 12.089 27093 Z= 0.318 Chirality : 0.047 0.383 3221 Planarity : 0.005 0.057 3456 Dihedral : 6.722 59.914 2912 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.06 % Favored : 90.89 % Rotamer: Outliers : 4.50 % Allowed : 20.98 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -1.89 (0.17), residues: 2438 helix: -1.55 (0.38), residues: 169 sheet: -0.51 (0.17), residues: 888 loop : -1.76 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 382 HIS 0.004 0.001 HIS L 518 PHE 0.024 0.002 PHE L 479 TYR 0.013 0.001 TYR H 455 ARG 0.013 0.001 ARG B 443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 242 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 345 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 ASP cc_start: 0.5970 (m-30) cc_final: 0.5535 (m-30) REVERT: A 537 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8903 (m) REVERT: B 489 MET cc_start: 0.8364 (mtt) cc_final: 0.8083 (mtt) REVERT: B 510 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7964 (pp30) REVERT: C 391 LYS cc_start: 0.7613 (tmtt) cc_final: 0.6656 (ttmm) REVERT: D 414 CYS cc_start: 0.5467 (OUTLIER) cc_final: 0.5241 (m) REVERT: E 449 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8358 (mm) REVERT: F 449 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7990 (pp) REVERT: F 453 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7229 (p0) REVERT: G 364 LYS cc_start: 0.8020 (tptt) cc_final: 0.7257 (tppt) REVERT: H 380 ILE cc_start: 0.1189 (mm) cc_final: 0.0684 (tt) REVERT: H 395 ASN cc_start: 0.4908 (t0) cc_final: 0.4429 (t0) REVERT: K 418 TRP cc_start: 0.5931 (OUTLIER) cc_final: 0.2817 (t-100) REVERT: K 467 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7729 (tpp80) REVERT: L 450 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5693 (m90) REVERT: L 451 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8123 (ptm160) REVERT: R 81 TYR cc_start: 0.4996 (m-80) cc_final: 0.4469 (m-80) REVERT: R 90 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7903 (tm-30) outliers start: 99 outliers final: 85 residues processed: 309 average time/residue: 0.3748 time to fit residues: 172.1411 Evaluate side-chains 326 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 232 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain B residue 518 HIS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 CYS Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 545 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 453 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 545 ASN Chi-restraints excluded: chain E residue 553 ASP Chi-restraints excluded: chain E residue 561 LEU Chi-restraints excluded: chain F residue 358 PHE Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 453 ASP Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 536 CYS Chi-restraints excluded: chain F residue 545 ASN Chi-restraints excluded: chain F residue 551 THR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 424 PHE Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 477 THR Chi-restraints excluded: chain G residue 503 SER Chi-restraints excluded: chain G residue 533 THR Chi-restraints excluded: chain H residue 358 PHE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 456 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 502 THR Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 537 VAL Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain H residue 545 ASN Chi-restraints excluded: chain H residue 550 ARG Chi-restraints excluded: chain H residue 562 TYR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 12 CYS Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 392 THR Chi-restraints excluded: chain K residue 418 TRP Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain L residue 353 SER Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 450 HIS Chi-restraints excluded: chain L residue 451 ARG Chi-restraints excluded: chain L residue 502 THR Chi-restraints excluded: chain L residue 552 VAL Chi-restraints excluded: chain L residue 561 LEU Chi-restraints excluded: chain L residue 567 VAL Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 108 MET Chi-restraints excluded: chain R residue 111 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 176 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 196 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN C 545 ASN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN K 490 GLN ** L 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.202047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132463 restraints weight = 27273.390| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 4.49 r_work: 0.3323 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19802 Z= 0.172 Angle : 0.614 10.753 27093 Z= 0.306 Chirality : 0.046 0.363 3221 Planarity : 0.005 0.056 3456 Dihedral : 6.432 59.639 2911 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.37 % Favored : 91.59 % Rotamer: Outliers : 4.09 % Allowed : 21.57 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.24 % 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: -1.68 (0.17), residues: 2438 helix: -1.54 (0.38), residues: 169 sheet: -0.37 (0.17), residues: 895 loop : -1.59 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 382 HIS 0.004 0.001 HIS L 518 PHE 0.023 0.001 PHE E 424 TYR 0.014 0.001 TYR E 500 ARG 0.012 0.000 ARG B 443 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5252.36 seconds wall clock time: 95 minutes 27.74 seconds (5727.74 seconds total)