Starting phenix.real_space_refine on Sat Mar 16 17:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt6_13619/03_2024/7pt6_13619_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 7 Type Number sf(0) Gaussians Zn 14 6.06 5 P 44 5.49 5 Mg 14 5.21 5 S 348 5.16 5 C 46800 2.51 5 N 12922 2.21 5 O 14216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 221": "OE1" <-> "OE2" Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 495": "OD1" <-> "OD2" Residue "2 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 689": "OE1" <-> "OE2" Residue "2 GLU 709": "OE1" <-> "OE2" Residue "2 TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 782": "OD1" <-> "OD2" Residue "3 ASP 40": "OD1" <-> "OD2" Residue "3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 358": "OD1" <-> "OD2" Residue "3 TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 703": "OE1" <-> "OE2" Residue "4 GLU 189": "OE1" <-> "OE2" Residue "4 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 273": "OD1" <-> "OD2" Residue "4 ASP 278": "OD1" <-> "OD2" Residue "4 TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 295": "OE1" <-> "OE2" Residue "4 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 341": "OD1" <-> "OD2" Residue "4 GLU 359": "OE1" <-> "OE2" Residue "4 GLU 434": "OE1" <-> "OE2" Residue "4 ASP 462": "OD1" <-> "OD2" Residue "4 ASP 471": "OD1" <-> "OD2" Residue "4 GLU 516": "OE1" <-> "OE2" Residue "4 GLU 532": "OE1" <-> "OE2" Residue "4 ASP 693": "OD1" <-> "OD2" Residue "4 GLU 719": "OE1" <-> "OE2" Residue "4 TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 799": "OE1" <-> "OE2" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 GLU 818": "OE1" <-> "OE2" Residue "4 TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 21": "OD1" <-> "OD2" Residue "5 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 402": "OD1" <-> "OD2" Residue "5 GLU 465": "OE1" <-> "OE2" Residue "5 ASP 489": "OD1" <-> "OD2" Residue "5 PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 378": "OD1" <-> "OD2" Residue "6 ASP 393": "OD1" <-> "OD2" Residue "6 TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 657": "OE1" <-> "OE2" Residue "6 PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 801": "OE1" <-> "OE2" Residue "6 GLU 818": "OE1" <-> "OE2" Residue "7 ASP 23": "OD1" <-> "OD2" Residue "7 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 74": "OE1" <-> "OE2" Residue "7 ASP 179": "OD1" <-> "OD2" Residue "7 ASP 187": "OD1" <-> "OD2" Residue "7 ASP 233": "OD1" <-> "OD2" Residue "7 GLU 256": "OE1" <-> "OE2" Residue "7 ASP 441": "OD1" <-> "OD2" Residue "7 GLU 525": "OE1" <-> "OE2" Residue "7 PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 709": "OD1" <-> "OD2" Residue "8 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 288": "OE1" <-> "OE2" Residue "8 ASP 325": "OD1" <-> "OD2" Residue "8 GLU 331": "OE1" <-> "OE2" Residue "8 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 340": "OE1" <-> "OE2" Residue "8 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 433": "OE1" <-> "OE2" Residue "8 PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 447": "OE1" <-> "OE2" Residue "9 PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 256": "OD1" <-> "OD2" Residue "9 ASP 257": "OD1" <-> "OD2" Residue "9 ASP 292": "OD1" <-> "OD2" Residue "9 PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 495": "OD1" <-> "OD2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "B TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "D ASP 462": "OD1" <-> "OD2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D GLU 532": "OE1" <-> "OE2" Residue "D ASP 693": "OD1" <-> "OD2" Residue "D GLU 719": "OE1" <-> "OE2" Residue "D TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 799": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E ASP 489": "OD1" <-> "OD2" Residue "E PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 378": "OD1" <-> "OD2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F GLU 818": "OE1" <-> "OE2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "G TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G ASP 441": "OD1" <-> "OD2" Residue "G GLU 525": "OE1" <-> "OE2" Residue "G PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 709": "OD1" <-> "OD2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 288": "OE1" <-> "OE2" Residue "H ASP 325": "OD1" <-> "OD2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 340": "OE1" <-> "OE2" Residue "H TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 433": "OE1" <-> "OE2" Residue "H PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 447": "OE1" <-> "OE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 256": "OD1" <-> "OD2" Residue "I ASP 257": "OD1" <-> "OD2" Residue "I ASP 292": "OD1" <-> "OD2" Residue "I PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74358 Number of models: 1 Model: "" Number of chains: 34 Chain: "1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 4989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4989 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 3 Chain: "3" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5000 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 31, 'TRANS': 605} Chain breaks: 6 Chain: "4" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5323 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 24, 'TRANS': 643} Chain breaks: 1 Chain: "5" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5037 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 28, 'TRANS': 615} Chain breaks: 3 Chain: "6" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5048 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 22, 'TRANS': 614} Chain breaks: 3 Chain: "7" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5370 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 30, 'TRANS': 652} Chain breaks: 3 Chain: "8" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3292 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 3 Chain: "9" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2846 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4989 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 25, 'TRANS': 603} Chain breaks: 3 Chain: "C" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5000 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 31, 'TRANS': 605} Chain breaks: 6 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5323 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 24, 'TRANS': 643} Chain breaks: 1 Chain: "E" Number of atoms: 5037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5037 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 28, 'TRANS': 615} Chain breaks: 3 Chain: "F" Number of atoms: 5048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5048 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 22, 'TRANS': 614} Chain breaks: 3 Chain: "G" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5370 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 30, 'TRANS': 652} Chain breaks: 3 Chain: "H" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3292 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 3 Chain: "I" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2846 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 4 Chain: "2" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1351 SG CYS 2 341 137.996 104.928 81.454 1.00 60.30 S ATOM 1374 SG CYS 2 344 141.360 106.945 81.174 1.00 70.03 S ATOM 1532 SG CYS 2 364 139.558 106.448 84.627 1.00 66.27 S ATOM 1553 SG CYS 2 367 139.058 108.885 81.675 1.00 80.44 S ATOM 11445 SG CYS 4 349 96.721 113.797 100.685 1.00 32.18 S ATOM 11466 SG CYS 4 352 94.899 115.600 103.370 1.00 37.99 S ATOM 11613 SG CYS 4 371 94.199 116.359 99.562 1.00 49.73 S ATOM 11655 SG CYS 4 376 97.117 117.736 101.511 1.00 61.15 S ATOM 16618 SG CYS 5 183 130.225 111.035 59.140 1.00 8.16 S ATOM 16643 SG CYS 5 186 131.869 114.372 57.973 1.00 15.58 S ATOM 16833 SG CYS 5 211 133.344 112.330 60.871 1.00 8.02 S ATOM 16868 SG CYS 5 236 130.173 114.274 61.225 1.00 25.49 S ATOM 21637 SG CYS 6 311 115.922 110.400 98.890 1.00 81.58 S ATOM 21659 SG CYS 6 314 116.760 111.748 102.288 1.00 86.40 S ATOM 21816 SG CYS 6 333 113.228 112.341 100.851 1.00 74.61 S ATOM 21850 SG CYS 6 338 116.237 114.099 99.346 1.00 90.37 S ATOM 27172 SG CYS 7 262 85.562 118.187 74.754 1.00 6.57 S ATOM 27195 SG CYS 7 265 84.688 120.906 72.198 1.00 7.29 S ATOM 27349 SG CYS 7 284 87.648 118.589 71.573 1.00 7.12 S ATOM 27386 SG CYS 7 289 87.782 121.293 74.197 1.00 18.98 S ATOM 32363 SG CYS 8 223 193.292 97.256 108.026 1.00 94.06 S ATOM 32376 SG CYS 8 225 191.659 99.254 106.474 1.00 92.69 S ATOM 32738 SG CYS 8 293 194.053 98.925 104.241 1.00 65.25 S ATOM 36593 SG CYS 9 661 205.899 113.491 79.327 1.00 51.12 S ATOM 36616 SG CYS 9 664 206.265 117.291 78.438 1.00 48.86 S ATOM 38276 SG CYS B 341 108.239 119.330 82.035 1.00 60.30 S ATOM 38299 SG CYS B 344 104.865 117.329 81.772 1.00 70.03 S ATOM 38457 SG CYS B 364 106.767 117.685 85.188 1.00 66.27 S ATOM 38478 SG CYS B 367 107.177 115.368 82.128 1.00 80.44 S ATOM 48370 SG CYS D 349 150.067 109.690 99.731 1.00 32.18 S ATOM 48391 SG CYS D 352 151.963 107.783 102.291 1.00 37.99 S ATOM 48538 SG CYS D 371 152.555 107.175 98.437 1.00 49.73 S ATOM 48580 SG CYS D 376 149.692 105.721 100.412 1.00 61.15 S ATOM 53543 SG CYS E 183 115.426 114.103 59.306 1.00 8.16 S ATOM 53568 SG CYS E 186 113.748 110.814 58.055 1.00 15.58 S ATOM 53758 SG CYS E 211 112.356 112.739 61.072 1.00 8.02 S ATOM 53793 SG CYS E 236 115.535 110.784 61.259 1.00 25.49 S ATOM 58562 SG CYS F 311 130.842 113.153 98.619 1.00 81.58 S ATOM 58584 SG CYS F 314 130.099 111.672 101.984 1.00 86.40 S ATOM 58741 SG CYS F 333 133.589 111.137 100.425 1.00 74.61 S ATOM 58775 SG CYS F 338 130.537 109.439 98.938 1.00 90.37 S ATOM 64097 SG CYS G 262 160.469 106.319 73.340 1.00 6.57 S ATOM 64120 SG CYS G 265 161.269 103.703 70.656 1.00 7.29 S ATOM 64274 SG CYS G 284 158.295 106.042 70.206 1.00 7.12 S ATOM 64311 SG CYS G 289 158.232 103.236 72.724 1.00 18.98 S ATOM 69288 SG CYS H 223 53.744 126.028 110.192 1.00 94.06 S ATOM 69301 SG CYS H 225 55.327 124.088 108.518 1.00 92.69 S ATOM 69663 SG CYS H 293 52.868 124.502 106.372 1.00 65.25 S ATOM 73518 SG CYS I 661 40.286 110.831 81.482 1.00 51.12 S ATOM 73541 SG CYS I 664 39.890 107.063 80.475 1.00 48.86 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN 61104 " occ=0.50 residue: pdb="ZN ZN F1104 " occ=0.50 Time building chain proxies: 28.78, per 1000 atoms: 0.39 Number of scatterers: 74358 At special positions: 0 Unit cell: (248.04, 224.72, 154.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 14 29.99 S 348 16.00 P 44 15.00 Mg 14 11.99 O 14216 8.00 N 12922 7.00 C 46800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.42 Conformation dependent library (CDL) restraints added in 9.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 367 " pdb=" ZN 41002 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 41002 " - pdb=" SG CYS 4 349 " pdb=" ZN 51002 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 183 " pdb=" ZN 61104 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61104 " - pdb=" SG CYS 6 333 " pdb=" ZN 7 904 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 904 " - pdb=" SG CYS 7 262 " pdb=" ZN 81003 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 293 " pdb="ZN ZN 81003 " - pdb=" ND1 HIS 8 348 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 223 " pdb="ZN ZN 81003 " - pdb=" SG CYS 8 225 " pdb=" ZN 91101 " pdb="ZN ZN 91101 " - pdb=" NE2 HIS 9 674 " pdb="ZN ZN 91101 " - pdb=" ND1 HIS 9 680 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 664 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 661 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 344 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 364 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 367 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 352 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 376 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 371 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 349 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 236 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 211 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 186 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 183 " pdb=" ZN F1104 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 338 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 311 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 314 " pdb="ZN ZN F1104 " - pdb=" SG CYS F 333 " pdb=" ZN G 904 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 265 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 289 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 284 " pdb="ZN ZN G 904 " - pdb=" SG CYS G 262 " pdb=" ZN H1003 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 293 " pdb="ZN ZN H1003 " - pdb=" ND1 HIS H 348 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 223 " pdb="ZN ZN H1003 " - pdb=" SG CYS H 225 " pdb=" ZN I1101 " pdb="ZN ZN I1101 " - pdb=" NE2 HIS I 674 " pdb="ZN ZN I1101 " - pdb=" ND1 HIS I 680 " pdb="ZN ZN I1101 " - pdb=" SG CYS I 664 " pdb="ZN ZN I1101 " - pdb=" SG CYS I 661 " Number of angles added : 68 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 346 helices and 92 sheets defined 36.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.07 Creating SS restraints... Processing helix chain '2' and resid 183 through 186 No H-bonds generated for 'chain '2' and resid 183 through 186' Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 217 removed outlier: 3.803A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 237 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 270 through 282 removed outlier: 3.565A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 478 through 489 removed outlier: 3.780A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 614 through 626 Processing helix chain '2' and resid 663 through 665 No H-bonds generated for 'chain '2' and resid 663 through 665' Processing helix chain '2' and resid 671 through 676 removed outlier: 3.780A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 760 through 773 Processing helix chain '2' and resid 780 through 800 removed outlier: 4.910A pdb=" N ASP 2 784 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS 2 785 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 2 796 " --> pdb=" O LEU 2 793 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE 2 798 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER 2 799 " --> pdb=" O GLU 2 796 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR 2 800 " --> pdb=" O SER 2 797 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 Processing helix chain '2' and resid 831 through 847 Processing helix chain '2' and resid 853 through 858 removed outlier: 3.767A pdb=" N GLN 2 856 " --> pdb=" O VAL 2 853 " (cutoff:3.500A) Processing helix chain '2' and resid 861 through 863 No H-bonds generated for 'chain '2' and resid 861 through 863' Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 37 through 55 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 344 through 354 Processing helix chain '3' and resid 357 through 365 removed outlier: 4.597A pdb=" N PHE 3 360 " --> pdb=" O LYS 3 357 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN 3 365 " --> pdb=" O ILE 3 362 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 480 through 492 removed outlier: 3.792A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 533 Processing helix chain '3' and resid 537 through 542 removed outlier: 3.738A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 688 removed outlier: 4.126A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 738 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 213 through 215 No H-bonds generated for 'chain '4' and resid 213 through 215' Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 removed outlier: 3.874A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 263 removed outlier: 4.049A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 Processing helix chain '4' and resid 294 through 297 No H-bonds generated for 'chain '4' and resid 294 through 297' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 386 through 388 No H-bonds generated for 'chain '4' and resid 386 through 388' Processing helix chain '4' and resid 478 through 480 No H-bonds generated for 'chain '4' and resid 478 through 480' Processing helix chain '4' and resid 482 through 491 Processing helix chain '4' and resid 503 through 513 Processing helix chain '4' and resid 518 through 525 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 644 through 650 removed outlier: 3.806A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 678 through 680 No H-bonds generated for 'chain '4' and resid 678 through 680' Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 699 No H-bonds generated for 'chain '4' and resid 696 through 699' Processing helix chain '4' and resid 714 through 728 removed outlier: 3.617A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 removed outlier: 3.512A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 777 Processing helix chain '4' and resid 796 through 811 Processing helix chain '4' and resid 819 through 832 Processing helix chain '4' and resid 835 through 837 No H-bonds generated for 'chain '4' and resid 835 through 837' Processing helix chain '4' and resid 847 through 849 No H-bonds generated for 'chain '4' and resid 847 through 849' Processing helix chain '5' and resid 24 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 106 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 245 through 247 No H-bonds generated for 'chain '5' and resid 245 through 247' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 372 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 498 removed outlier: 3.565A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 549 Processing helix chain '5' and resid 562 through 575 Processing helix chain '5' and resid 580 through 588 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 639 removed outlier: 3.772A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 3.975A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 686 Processing helix chain '5' and resid 690 through 693 No H-bonds generated for 'chain '5' and resid 690 through 693' Processing helix chain '6' and resid 106 through 121 Processing helix chain '6' and resid 135 through 145 Processing helix chain '6' and resid 155 through 172 removed outlier: 3.991A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 191 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 196 No H-bonds generated for 'chain '6' and resid 194 through 196' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 407 through 409 No H-bonds generated for 'chain '6' and resid 407 through 409' Processing helix chain '6' and resid 501 through 506 Processing helix chain '6' and resid 510 through 521 Processing helix chain '6' and resid 525 through 531 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 588 removed outlier: 3.655A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 646 through 658 removed outlier: 3.519A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 685 through 687 No H-bonds generated for 'chain '6' and resid 685 through 687' Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 removed outlier: 4.081A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 748 through 760 removed outlier: 4.237A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 783 removed outlier: 3.617A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 814 Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 62 through 72 Processing helix chain '7' and resid 82 through 94 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 123 removed outlier: 3.711A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 164 Processing helix chain '7' and resid 178 through 188 Processing helix chain '7' and resid 287 through 291 Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 364 through 366 No H-bonds generated for 'chain '7' and resid 364 through 366' Processing helix chain '7' and resid 388 through 390 No H-bonds generated for 'chain '7' and resid 388 through 390' Processing helix chain '7' and resid 395 through 405 Processing helix chain '7' and resid 410 through 416 Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 543 Processing helix chain '7' and resid 570 through 572 No H-bonds generated for 'chain '7' and resid 570 through 572' Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 607 through 621 Processing helix chain '7' and resid 635 through 647 removed outlier: 3.581A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 673 removed outlier: 4.207A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 722 Processing helix chain '8' and resid 13 through 25 removed outlier: 3.910A pdb=" N GLU 8 17 " --> pdb=" O PRO 8 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU 8 18 " --> pdb=" O GLU 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 27 through 29 No H-bonds generated for 'chain '8' and resid 27 through 29' Processing helix chain '8' and resid 84 through 96 Processing helix chain '8' and resid 128 through 131 No H-bonds generated for 'chain '8' and resid 128 through 131' Processing helix chain '8' and resid 137 through 157 Processing helix chain '8' and resid 287 through 290 No H-bonds generated for 'chain '8' and resid 287 through 290' Processing helix chain '8' and resid 298 through 312 removed outlier: 3.956A pdb=" N VAL 8 307 " --> pdb=" O SER 8 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE 8 308 " --> pdb=" O VAL 8 305 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU 8 312 " --> pdb=" O LEU 8 309 " (cutoff:3.500A) Processing helix chain '8' and resid 325 through 336 removed outlier: 3.630A pdb=" N ILE 8 335 " --> pdb=" O GLU 8 331 " (cutoff:3.500A) Processing helix chain '8' and resid 338 through 348 removed outlier: 3.743A pdb=" N LEU 8 347 " --> pdb=" O LYS 8 343 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS 8 348 " --> pdb=" O CYS 8 344 " (cutoff:3.500A) Processing helix chain '8' and resid 369 through 383 removed outlier: 3.931A pdb=" N GLU 8 380 " --> pdb=" O LEU 8 376 " (cutoff:3.500A) Processing helix chain '8' and resid 392 through 402 Processing helix chain '8' and resid 427 through 449 Processing helix chain '8' and resid 460 through 464 Processing helix chain '8' and resid 467 through 469 No H-bonds generated for 'chain '8' and resid 467 through 469' Processing helix chain '9' and resid 112 through 115 No H-bonds generated for 'chain '9' and resid 112 through 115' Processing helix chain '9' and resid 138 through 156 Processing helix chain '9' and resid 190 through 194 Processing helix chain '9' and resid 204 through 214 Processing helix chain '9' and resid 234 through 242 Processing helix chain '9' and resid 285 through 288 Processing helix chain '9' and resid 320 through 332 removed outlier: 4.080A pdb=" N LYS 9 325 " --> pdb=" O LYS 9 321 " (cutoff:3.500A) Processing helix chain '9' and resid 334 through 343 Processing helix chain '9' and resid 350 through 352 No H-bonds generated for 'chain '9' and resid 350 through 352' Processing helix chain '9' and resid 374 through 384 Processing helix chain '9' and resid 522 through 530 removed outlier: 3.500A pdb=" N SER 9 528 " --> pdb=" O MET 9 524 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG 9 529 " --> pdb=" O LYS 9 525 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU 9 530 " --> pdb=" O SER 9 526 " (cutoff:3.500A) Processing helix chain '9' and resid 671 through 674 No H-bonds generated for 'chain '9' and resid 671 through 674' Processing helix chain '9' and resid 678 through 685 Processing helix chain '9' and resid 692 through 700 removed outlier: 3.764A pdb=" N LEU 9 696 " --> pdb=" O ALA 9 692 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU 9 698 " --> pdb=" O ASP 9 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.803A pdb=" N THR B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 270 through 282 removed outlier: 3.564A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 478 through 489 removed outlier: 3.780A pdb=" N ARG B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 595 through 598 No H-bonds generated for 'chain 'B' and resid 595 through 598' Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 671 through 676 removed outlier: 3.780A pdb=" N ARG B 676 " --> pdb=" O PRO B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 705 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 780 through 800 removed outlier: 4.910A pdb=" N ASP B 784 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 796 " --> pdb=" O LEU B 793 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 798 " --> pdb=" O ARG B 795 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 799 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 800 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.767A pdb=" N GLN B 856 " --> pdb=" O VAL B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 863 No H-bonds generated for 'chain 'B' and resid 861 through 863' Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 118 through 136 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 344 through 354 Processing helix chain 'C' and resid 357 through 365 removed outlier: 4.596A pdb=" N PHE C 360 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN C 365 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 480 through 492 removed outlier: 3.792A pdb=" N ALA C 485 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.738A pdb=" N ARG C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'C' and resid 673 through 688 removed outlier: 4.126A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 723 through 738 Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.874A pdb=" N LEU D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.050A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 Processing helix chain 'D' and resid 294 through 297 No H-bonds generated for 'chain 'D' and resid 294 through 297' Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 503 through 513 Processing helix chain 'D' and resid 518 through 525 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 644 through 650 removed outlier: 3.807A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 688 through 692 Processing helix chain 'D' and resid 696 through 699 No H-bonds generated for 'chain 'D' and resid 696 through 699' Processing helix chain 'D' and resid 714 through 728 removed outlier: 3.617A pdb=" N LEU D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 757 removed outlier: 3.512A pdb=" N MET D 749 " --> pdb=" O GLU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 777 Processing helix chain 'D' and resid 796 through 811 Processing helix chain 'D' and resid 819 through 832 Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 847 through 849 No H-bonds generated for 'chain 'D' and resid 847 through 849' Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 106 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 351 through 361 Processing helix chain 'E' and resid 366 through 372 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 487 through 498 removed outlier: 3.565A pdb=" N VAL E 491 " --> pdb=" O ASP E 487 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 498 " --> pdb=" O HIS E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 549 Processing helix chain 'E' and resid 562 through 575 Processing helix chain 'E' and resid 580 through 588 Processing helix chain 'E' and resid 596 through 609 Processing helix chain 'E' and resid 616 through 639 removed outlier: 3.773A pdb=" N GLU E 639 " --> pdb=" O ILE E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 667 removed outlier: 3.974A pdb=" N GLU E 667 " --> pdb=" O LEU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 686 Processing helix chain 'E' and resid 690 through 693 No H-bonds generated for 'chain 'E' and resid 690 through 693' Processing helix chain 'F' and resid 106 through 121 Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 155 through 172 removed outlier: 3.990A pdb=" N MET F 160 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG F 161 " --> pdb=" O HIS F 157 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 164 " --> pdb=" O MET F 160 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA F 167 " --> pdb=" O ASN F 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 191 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 407 through 409 No H-bonds generated for 'chain 'F' and resid 407 through 409' Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 510 through 521 Processing helix chain 'F' and resid 525 through 531 Processing helix chain 'F' and resid 541 through 552 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.655A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 627 through 630 No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 646 through 658 removed outlier: 3.520A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 687 No H-bonds generated for 'chain 'F' and resid 685 through 687' Processing helix chain 'F' and resid 695 through 698 No H-bonds generated for 'chain 'F' and resid 695 through 698' Processing helix chain 'F' and resid 703 through 708 removed outlier: 4.081A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 736 Processing helix chain 'F' and resid 748 through 760 removed outlier: 4.238A pdb=" N THR F 760 " --> pdb=" O LYS F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 783 removed outlier: 3.618A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 814 Processing helix chain 'F' and resid 821 through 834 Processing helix chain 'G' and resid 14 through 27 Processing helix chain 'G' and resid 62 through 72 Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.710A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 164 Processing helix chain 'G' and resid 178 through 188 Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 364 through 366 No H-bonds generated for 'chain 'G' and resid 364 through 366' Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 395 through 405 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 512 through 515 No H-bonds generated for 'chain 'G' and resid 512 through 515' Processing helix chain 'G' and resid 526 through 528 No H-bonds generated for 'chain 'G' and resid 526 through 528' Processing helix chain 'G' and resid 531 through 543 Processing helix chain 'G' and resid 570 through 572 No H-bonds generated for 'chain 'G' and resid 570 through 572' Processing helix chain 'G' and resid 580 through 583 No H-bonds generated for 'chain 'G' and resid 580 through 583' Processing helix chain 'G' and resid 588 through 593 Processing helix chain 'G' and resid 607 through 621 Processing helix chain 'G' and resid 635 through 647 removed outlier: 3.581A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 673 removed outlier: 4.207A pdb=" N TYR G 659 " --> pdb=" O ALA G 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 686 through 702 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'H' and resid 13 through 25 removed outlier: 3.910A pdb=" N GLU H 17 " --> pdb=" O PRO H 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 84 through 96 Processing helix chain 'H' and resid 128 through 131 No H-bonds generated for 'chain 'H' and resid 128 through 131' Processing helix chain 'H' and resid 137 through 157 Processing helix chain 'H' and resid 287 through 290 No H-bonds generated for 'chain 'H' and resid 287 through 290' Processing helix chain 'H' and resid 298 through 312 removed outlier: 3.956A pdb=" N VAL H 307 " --> pdb=" O SER H 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 308 " --> pdb=" O VAL H 305 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU H 312 " --> pdb=" O LEU H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 336 removed outlier: 3.630A pdb=" N ILE H 335 " --> pdb=" O GLU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.743A pdb=" N LEU H 347 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS H 348 " --> pdb=" O CYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 383 removed outlier: 3.931A pdb=" N GLU H 380 " --> pdb=" O LEU H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 402 Processing helix chain 'H' and resid 427 through 449 Processing helix chain 'H' and resid 460 through 464 Processing helix chain 'H' and resid 467 through 469 No H-bonds generated for 'chain 'H' and resid 467 through 469' Processing helix chain 'I' and resid 112 through 115 No H-bonds generated for 'chain 'I' and resid 112 through 115' Processing helix chain 'I' and resid 138 through 156 Processing helix chain 'I' and resid 190 through 194 Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 234 through 242 Processing helix chain 'I' and resid 285 through 288 Processing helix chain 'I' and resid 320 through 332 removed outlier: 4.081A pdb=" N LYS I 325 " --> pdb=" O LYS I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 343 Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 374 through 384 Processing helix chain 'I' and resid 522 through 530 removed outlier: 4.101A pdb=" N ARG I 529 " --> pdb=" O LYS I 525 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU I 530 " --> pdb=" O SER I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 674 No H-bonds generated for 'chain 'I' and resid 671 through 674' Processing helix chain 'I' and resid 678 through 685 Processing helix chain 'I' and resid 692 through 700 removed outlier: 3.764A pdb=" N LEU I 696 " --> pdb=" O ALA I 692 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU I 698 " --> pdb=" O ASP I 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 423 through 430 removed outlier: 3.774A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N SER 2 455 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA 2 448 " --> pdb=" O ASN 2 433 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 339 through 341 Processing sheet with id= C, first strand: chain '2' and resid 679 through 683 Processing sheet with id= D, first strand: chain '2' and resid 579 through 582 Processing sheet with id= E, first strand: chain '2' and resid 628 through 633 Processing sheet with id= F, first strand: chain '2' and resid 331 through 336 removed outlier: 6.663A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 95 through 99 removed outlier: 7.073A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain '3' and resid 165 through 167 removed outlier: 7.920A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 208 through 213 Processing sheet with id= J, first strand: chain '3' and resid 273 through 279 removed outlier: 3.789A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 545 through 549 Processing sheet with id= L, first strand: chain '3' and resid 494 through 496 Processing sheet with id= M, first strand: chain '3' and resid 193 through 198 removed outlier: 6.435A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 414 through 420 removed outlier: 3.624A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS 4 324 " --> pdb=" O PHE 4 439 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 357 through 359 removed outlier: 6.712A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 347 through 349 Processing sheet with id= Q, first strand: chain '4' and resid 550 through 552 removed outlier: 4.161A pdb=" N GLY 4 556 " --> pdb=" O PHE 4 552 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 704 through 708 Processing sheet with id= S, first strand: chain '4' and resid 604 through 607 Processing sheet with id= T, first strand: chain '4' and resid 653 through 658 Processing sheet with id= U, first strand: chain '5' and resid 60 through 64 removed outlier: 6.477A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '5' and resid 291 through 298 removed outlier: 3.982A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 189 through 193 removed outlier: 4.585A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 552 through 556 Processing sheet with id= Y, first strand: chain '5' and resid 501 through 505 Processing sheet with id= Z, first strand: chain '5' and resid 173 through 178 removed outlier: 6.590A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 452 through 454 removed outlier: 3.636A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '6' and resid 150 through 154 removed outlier: 6.359A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain '6' and resid 394 through 400 removed outlier: 6.632A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.295A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 12.236A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AE, first strand: chain '6' and resid 711 through 715 Processing sheet with id= AF, first strand: chain '6' and resid 611 through 613 Processing sheet with id= AG, first strand: chain '6' and resid 660 through 662 Processing sheet with id= AH, first strand: chain '6' and resid 301 through 306 removed outlier: 6.777A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '7' and resid 77 through 81 removed outlier: 6.052A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain '7' and resid 330 through 336 removed outlier: 3.763A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '7' and resid 268 through 272 Processing sheet with id= AL, first strand: chain '7' and resid 596 through 600 Processing sheet with id= AM, first strand: chain '7' and resid 495 through 500 removed outlier: 4.378A pdb=" N GLU 7 505 " --> pdb=" O ASP 7 500 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 545 through 550 Processing sheet with id= AO, first strand: chain '7' and resid 252 through 257 removed outlier: 6.736A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '8' and resid 106 through 112 removed outlier: 6.744A pdb=" N VAL 8 119 " --> pdb=" O CYS 8 107 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA 8 109 " --> pdb=" O ILE 8 117 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE 8 117 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG 8 111 " --> pdb=" O GLN 8 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN 8 115 " --> pdb=" O ARG 8 111 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL 8 116 " --> pdb=" O ILE 8 78 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU 8 35 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '8' and resid 169 through 172 Processing sheet with id= AR, first strand: chain '9' and resid 126 through 128 removed outlier: 6.138A pdb=" N ILE 9 172 " --> pdb=" O TYR 9 127 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS 9 200 " --> pdb=" O VAL 9 173 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR 9 175 " --> pdb=" O LYS 9 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP 9 202 " --> pdb=" O THR 9 175 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain '9' and resid 265 through 268 Processing sheet with id= AT, first strand: chain '9' and resid 659 through 661 removed outlier: 3.744A pdb=" N VAL 9 666 " --> pdb=" O CYS 9 661 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 423 through 430 removed outlier: 3.774A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR B 449 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU B 407 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 411 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N SER B 455 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 448 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE B 456 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU B 425 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= AW, first strand: chain 'B' and resid 679 through 683 Processing sheet with id= AX, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= AY, first strand: chain 'B' and resid 628 through 633 Processing sheet with id= AZ, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.663A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 95 through 99 removed outlier: 7.073A pdb=" N LYS C 154 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE C 98 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER C 156 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'C' and resid 165 through 167 removed outlier: 7.920A pdb=" N LEU C 166 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER C 181 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 178 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL C 297 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLY C 323 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS C 299 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE C 321 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 301 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR C 319 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'C' and resid 208 through 213 Processing sheet with id= BD, first strand: chain 'C' and resid 273 through 279 removed outlier: 3.789A pdb=" N LYS C 188 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN C 259 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL C 186 " --> pdb=" O GLN C 259 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'C' and resid 545 through 549 Processing sheet with id= BF, first strand: chain 'C' and resid 494 through 496 Processing sheet with id= BG, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.435A pdb=" N THR C 249 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 414 through 420 removed outlier: 3.623A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS D 324 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.711A pdb=" N SER D 390 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'D' and resid 347 through 349 Processing sheet with id= BK, first strand: chain 'D' and resid 550 through 552 removed outlier: 4.162A pdb=" N GLY D 556 " --> pdb=" O PHE D 552 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'D' and resid 704 through 708 Processing sheet with id= BM, first strand: chain 'D' and resid 604 through 607 Processing sheet with id= BN, first strand: chain 'D' and resid 653 through 658 Processing sheet with id= BO, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.477A pdb=" N GLN E 136 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL E 63 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 138 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'E' and resid 291 through 298 removed outlier: 3.981A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.586A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'E' and resid 552 through 556 Processing sheet with id= BS, first strand: chain 'E' and resid 501 through 505 Processing sheet with id= BT, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.589A pdb=" N LYS E 249 " --> pdb=" O THR E 177 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.636A pdb=" N GLY E 466 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN E 454 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU E 464 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.359A pdb=" N GLN F 264 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE F 153 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER F 266 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'F' and resid 394 through 400 removed outlier: 6.632A pdb=" N ARG F 360 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR F 297 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS F 358 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 14.295A pdb=" N TYR F 450 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 12.237A pdb=" N ASP F 378 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE F 452 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE F 380 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE F 454 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG F 382 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA F 456 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR F 398 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL F 459 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS F 396 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'F' and resid 309 through 311 Processing sheet with id= BY, first strand: chain 'F' and resid 711 through 715 Processing sheet with id= BZ, first strand: chain 'F' and resid 611 through 613 Processing sheet with id= CA, first strand: chain 'F' and resid 660 through 662 Processing sheet with id= CB, first strand: chain 'F' and resid 301 through 306 removed outlier: 6.777A pdb=" N ARG F 352 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.052A pdb=" N PHE G 201 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE G 80 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR G 203 " --> pdb=" O ILE G 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'G' and resid 330 through 336 removed outlier: 3.762A pdb=" N ARG G 247 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN G 316 " --> pdb=" O ILE G 245 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE G 245 " --> pdb=" O GLN G 316 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE G 354 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA G 378 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 356 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU G 376 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA G 358 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR G 374 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'G' and resid 268 through 272 Processing sheet with id= CF, first strand: chain 'G' and resid 596 through 600 Processing sheet with id= CG, first strand: chain 'G' and resid 495 through 500 removed outlier: 4.378A pdb=" N GLU G 505 " --> pdb=" O ASP G 500 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'G' and resid 545 through 550 Processing sheet with id= CI, first strand: chain 'G' and resid 252 through 257 removed outlier: 6.736A pdb=" N LYS G 306 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'H' and resid 106 through 112 removed outlier: 6.743A pdb=" N VAL H 119 " --> pdb=" O CYS H 107 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA H 109 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE H 117 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG H 111 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL H 116 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS H 51 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU H 35 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'H' and resid 169 through 172 Processing sheet with id= CL, first strand: chain 'I' and resid 126 through 128 removed outlier: 6.138A pdb=" N ILE I 172 " --> pdb=" O TYR I 127 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS I 200 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR I 175 " --> pdb=" O LYS I 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP I 202 " --> pdb=" O THR I 175 " (cutoff:3.500A) No H-bonds generated for sheet with id= CL Processing sheet with id= CM, first strand: chain 'I' and resid 265 through 268 Processing sheet with id= CN, first strand: chain 'I' and resid 659 through 661 removed outlier: 3.744A pdb=" N VAL I 666 " --> pdb=" O CYS I 661 " (cutoff:3.500A) 2665 hydrogen bonds defined for protein. 7647 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: 31.35 Time building geometry restraints manager: 25.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 18773 1.33 - 1.48: 22791 1.48 - 1.64: 33508 1.64 - 1.79: 77 1.79 - 1.94: 471 Bond restraints: 75620 Sorted by residual: bond pdb=" N PRO F 336 " pdb=" CD PRO F 336 " ideal model delta sigma weight residual 1.473 1.334 0.139 1.40e-02 5.10e+03 9.84e+01 bond pdb=" N PRO 6 336 " pdb=" CD PRO 6 336 " ideal model delta sigma weight residual 1.473 1.334 0.139 1.40e-02 5.10e+03 9.82e+01 bond pdb=" CA ARG F 350 " pdb=" C ARG F 350 " ideal model delta sigma weight residual 1.522 1.630 -0.109 1.43e-02 4.89e+03 5.77e+01 bond pdb=" CA ARG 6 350 " pdb=" C ARG 6 350 " ideal model delta sigma weight residual 1.522 1.630 -0.108 1.43e-02 4.89e+03 5.75e+01 bond pdb=" N PRO 5 418 " pdb=" CD PRO 5 418 " ideal model delta sigma weight residual 1.473 1.577 -0.104 1.40e-02 5.10e+03 5.55e+01 ... (remaining 75615 not shown) Histogram of bond angle deviations from ideal: 90.39 - 99.43: 28 99.43 - 108.48: 4281 108.48 - 117.52: 52080 117.52 - 126.56: 45084 126.56 - 135.60: 821 Bond angle restraints: 102294 Sorted by residual: angle pdb=" N PRO H 224 " pdb=" CA PRO H 224 " pdb=" C PRO H 224 " ideal model delta sigma weight residual 114.80 90.39 24.41 1.42e+00 4.96e-01 2.95e+02 angle pdb=" N PRO 8 224 " pdb=" CA PRO 8 224 " pdb=" C PRO 8 224 " ideal model delta sigma weight residual 114.80 90.43 24.37 1.42e+00 4.96e-01 2.94e+02 angle pdb=" N SER 2 797 " pdb=" CA SER 2 797 " pdb=" C SER 2 797 " ideal model delta sigma weight residual 111.36 122.29 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N SER B 797 " pdb=" CA SER B 797 " pdb=" C SER B 797 " ideal model delta sigma weight residual 111.36 122.25 -10.89 1.09e+00 8.42e-01 9.98e+01 angle pdb=" N SER 6 351 " pdb=" CA SER 6 351 " pdb=" C SER 6 351 " ideal model delta sigma weight residual 110.41 122.53 -12.12 1.23e+00 6.61e-01 9.72e+01 ... (remaining 102289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 45120 33.30 - 66.60: 1192 66.60 - 99.89: 120 99.89 - 133.19: 2 133.19 - 166.49: 6 Dihedral angle restraints: 46440 sinusoidal: 19238 harmonic: 27202 Sorted by residual: dihedral pdb=" CD ARG 9 176 " pdb=" NE ARG 9 176 " pdb=" CZ ARG 9 176 " pdb=" NH1 ARG 9 176 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG I 176 " pdb=" NE ARG I 176 " pdb=" CZ ARG I 176 " pdb=" NH1 ARG I 176 " ideal model delta sinusoidal sigma weight residual 0.00 -89.91 89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" C ARG 6 350 " pdb=" N ARG 6 350 " pdb=" CA ARG 6 350 " pdb=" CB ARG 6 350 " ideal model delta harmonic sigma weight residual -122.60 -137.46 14.86 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 46437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 10993 0.119 - 0.238: 595 0.238 - 0.357: 106 0.357 - 0.476: 16 0.476 - 0.595: 4 Chirality restraints: 11714 Sorted by residual: chirality pdb=" CA CYS 8 223 " pdb=" N CYS 8 223 " pdb=" C CYS 8 223 " pdb=" CB CYS 8 223 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA CYS H 223 " pdb=" N CYS H 223 " pdb=" C CYS H 223 " pdb=" CB CYS H 223 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA ARG 6 350 " pdb=" N ARG 6 350 " pdb=" C ARG 6 350 " pdb=" CB ARG 6 350 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 11711 not shown) Planarity restraints: 13096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 9 176 " 0.973 9.50e-02 1.11e+02 4.36e-01 1.18e+02 pdb=" NE ARG 9 176 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG 9 176 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG 9 176 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG 9 176 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 176 " -0.973 9.50e-02 1.11e+02 4.36e-01 1.18e+02 pdb=" NE ARG I 176 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG I 176 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG I 176 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG I 176 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 9 324 " 0.041 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C VAL 9 324 " -0.142 2.00e-02 2.50e+03 pdb=" O VAL 9 324 " 0.054 2.00e-02 2.50e+03 pdb=" N LYS 9 325 " 0.047 2.00e-02 2.50e+03 ... (remaining 13093 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 191 2.35 - 2.99: 37879 2.99 - 3.63: 110989 3.63 - 4.26: 177093 4.26 - 4.90: 296364 Nonbonded interactions: 622516 Sorted by model distance: nonbonded pdb=" NE2 GLN 8 432 " pdb=" CZ2 TRP 8 436 " model vdw 1.718 3.420 nonbonded pdb=" NE2 GLN H 432 " pdb=" CZ2 TRP H 436 " model vdw 1.719 3.420 nonbonded pdb=" N LYS D 204 " pdb=" OD1 ASP D 221 " model vdw 1.757 2.520 nonbonded pdb=" N LYS 4 204 " pdb=" OD1 ASP 4 221 " model vdw 1.757 2.520 nonbonded pdb=" CE LYS 9 380 " pdb=" OE1 GLN 9 383 " model vdw 1.821 3.440 ... (remaining 622511 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 '1' selection = chain 'A' } ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } ncs_group { reference = chain '8' selection = chain 'H' } ncs_group { reference = chain '9' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 13.290 Check model and map are aligned: 1.060 Set scattering table: 0.670 Process input model: 169.570 Find NCS groups from input model: 6.810 Set up NCS constraints: 0.700 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: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 196.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.006 0.139 75620 Z= 0.388 Angle : 1.065 24.406 102294 Z= 0.678 Chirality : 0.065 0.595 11714 Planarity : 0.009 0.436 13096 Dihedral : 15.098 166.490 28784 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.34 % Allowed : 1.90 % Favored : 97.76 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.09), residues: 9146 helix: 0.41 (0.09), residues: 3584 sheet: -0.92 (0.12), residues: 1592 loop : -0.60 (0.10), residues: 3970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 9 381 HIS 0.014 0.001 HIS 7 615 PHE 0.050 0.002 PHE C 735 TYR 0.047 0.002 TYR G 659 ARG 0.049 0.001 ARG 6 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1139 time to evaluate : 6.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 835 ASP cc_start: 0.7807 (m-30) cc_final: 0.7459 (m-30) REVERT: 3 151 HIS cc_start: 0.7195 (m-70) cc_final: 0.6896 (m90) REVERT: 3 731 ASN cc_start: 0.8216 (m-40) cc_final: 0.7957 (t0) REVERT: 4 382 MET cc_start: 0.8076 (mmm) cc_final: 0.7517 (mmp) REVERT: 5 153 SER cc_start: 0.8642 (p) cc_final: 0.8415 (p) REVERT: 5 393 MET cc_start: 0.8656 (mmp) cc_final: 0.8190 (mmp) REVERT: 7 573 ARG cc_start: 0.7298 (tpt90) cc_final: 0.6833 (tpp-160) REVERT: 7 602 ASP cc_start: 0.6296 (t0) cc_final: 0.6082 (p0) REVERT: 8 56 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7664 (tppt) REVERT: 8 146 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7706 (mm-30) REVERT: 8 367 ASN cc_start: 0.7228 (m-40) cc_final: 0.6582 (t0) REVERT: 8 441 TRP cc_start: 0.8595 (m100) cc_final: 0.8153 (m100) REVERT: 9 165 PHE cc_start: 0.6338 (m-80) cc_final: 0.5838 (m-80) REVERT: 9 273 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6608 (mm110) REVERT: 9 531 MET cc_start: 0.8641 (mmm) cc_final: 0.8312 (mmm) REVERT: 9 535 LYS cc_start: 0.5194 (ptmt) cc_final: 0.4506 (mmmt) REVERT: B 544 ASP cc_start: 0.7881 (m-30) cc_final: 0.7679 (m-30) REVERT: B 586 THR cc_start: 0.7476 (m) cc_final: 0.7101 (m) REVERT: B 653 ASN cc_start: 0.7739 (t0) cc_final: 0.7502 (t0) REVERT: D 199 MET cc_start: 0.8588 (mmt) cc_final: 0.8219 (mmt) REVERT: D 273 ASP cc_start: 0.7793 (m-30) cc_final: 0.7500 (m-30) REVERT: D 749 MET cc_start: 0.8283 (ttp) cc_final: 0.8072 (ttm) REVERT: D 811 MET cc_start: 0.8506 (ttp) cc_final: 0.8290 (ttp) REVERT: E 485 MET cc_start: 0.8571 (ttp) cc_final: 0.8238 (ttm) REVERT: E 514 ASN cc_start: 0.7748 (m-40) cc_final: 0.7359 (m-40) REVERT: E 583 MET cc_start: 0.4341 (mtt) cc_final: 0.4137 (mtm) REVERT: F 313 MET cc_start: 0.5389 (tpp) cc_final: 0.5085 (tpt) REVERT: F 644 MET cc_start: 0.8830 (ttm) cc_final: 0.8606 (ttp) REVERT: G 125 MET cc_start: 0.8952 (tpt) cc_final: 0.8364 (tpt) REVERT: G 449 LYS cc_start: 0.8497 (mttt) cc_final: 0.8205 (tptp) REVERT: G 687 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8174 (mtt90) REVERT: H 319 MET cc_start: 0.6598 (tpp) cc_final: 0.5287 (tpp) REVERT: H 386 PHE cc_start: 0.7965 (m-80) cc_final: 0.7588 (m-10) REVERT: I 129 ASP cc_start: 0.5662 (t70) cc_final: 0.5446 (t0) REVERT: I 292 ASP cc_start: 0.7633 (t0) cc_final: 0.7311 (t0) outliers start: 28 outliers final: 4 residues processed: 1162 average time/residue: 0.7391 time to fit residues: 1435.8368 Evaluate side-chains 788 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 783 time to evaluate : 6.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 574 LYS Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain G residue 687 ARG Chi-restraints excluded: chain H residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 777 optimal weight: 20.0000 chunk 698 optimal weight: 8.9990 chunk 387 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 470 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 chunk 721 optimal weight: 7.9990 chunk 279 optimal weight: 7.9990 chunk 438 optimal weight: 8.9990 chunk 537 optimal weight: 0.9990 chunk 836 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 551 GLN 2 809 HIS 3 417 GLN 3 670 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 327 ASN 4 380 ASN ** 4 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 797 GLN 5 284 ASN 5 499 GLN 5 524 ASN ** 5 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 560 HIS 5 576 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN 5 636 ASN 6 683 ASN 7 585 ASN ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 GLN ** 8 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 221 GLN 8 432 GLN 9 259 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN B 809 HIS C 722 ASN D 350 ASN ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN E 284 ASN E 539 ASN E 560 HIS E 561 ASN E 576 HIS E 581 ASN E 685 GLN F 117 GLN F 514 ASN F 669 HIS F 683 ASN G 585 ASN ** G 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 125 HIS I 339 GLN I 510 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 75620 Z= 0.236 Angle : 0.561 10.971 102294 Z= 0.287 Chirality : 0.043 0.339 11714 Planarity : 0.004 0.062 13096 Dihedral : 8.628 176.653 10445 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.07 % Allowed : 7.06 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.09), residues: 9146 helix: 0.72 (0.09), residues: 3622 sheet: -0.90 (0.12), residues: 1642 loop : -0.42 (0.10), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 356 HIS 0.010 0.001 HIS F 653 PHE 0.027 0.001 PHE 5 31 TYR 0.031 0.001 TYR 8 426 ARG 0.009 0.000 ARG G 593 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 850 time to evaluate : 6.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 547 THR cc_start: 0.8816 (m) cc_final: 0.8589 (m) REVERT: 2 764 MET cc_start: 0.7135 (mtm) cc_final: 0.6813 (mtm) REVERT: 2 835 ASP cc_start: 0.7794 (m-30) cc_final: 0.7477 (m-30) REVERT: 5 153 SER cc_start: 0.8816 (p) cc_final: 0.8586 (p) REVERT: 5 369 ILE cc_start: 0.8482 (tt) cc_final: 0.8269 (pt) REVERT: 5 393 MET cc_start: 0.8631 (mmp) cc_final: 0.8193 (mmp) REVERT: 5 543 GLN cc_start: 0.7358 (tt0) cc_final: 0.7059 (tt0) REVERT: 5 566 ILE cc_start: 0.8952 (mm) cc_final: 0.8737 (mm) REVERT: 6 117 GLN cc_start: 0.7915 (mt0) cc_final: 0.7589 (mt0) REVERT: 6 656 MET cc_start: 0.7669 (mtt) cc_final: 0.7423 (mtt) REVERT: 7 115 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: 7 182 ARG cc_start: 0.7805 (ttp80) cc_final: 0.5924 (ttp80) REVERT: 7 186 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: 7 675 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5288 (mtm) REVERT: 8 14 GLU cc_start: 0.7406 (pm20) cc_final: 0.7116 (pm20) REVERT: 8 146 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7808 (mm-30) REVERT: 9 378 PHE cc_start: 0.7280 (t80) cc_final: 0.6962 (t80) REVERT: 9 531 MET cc_start: 0.8663 (mmm) cc_final: 0.8299 (mmm) REVERT: 9 535 LYS cc_start: 0.5135 (ptmt) cc_final: 0.4502 (mmmt) REVERT: B 213 SER cc_start: 0.7991 (t) cc_final: 0.7725 (p) REVERT: B 237 MET cc_start: 0.7494 (mtm) cc_final: 0.7290 (mtp) REVERT: B 653 ASN cc_start: 0.7781 (t0) cc_final: 0.7567 (t0) REVERT: B 827 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6244 (tt0) REVERT: D 273 ASP cc_start: 0.7908 (m-30) cc_final: 0.7555 (m-30) REVERT: D 408 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8033 (p0) REVERT: D 614 LEU cc_start: 0.9188 (mt) cc_final: 0.8940 (mt) REVERT: E 352 GLU cc_start: 0.5803 (tp30) cc_final: 0.5408 (mm-30) REVERT: E 514 ASN cc_start: 0.7813 (m-40) cc_final: 0.7394 (m-40) REVERT: F 313 MET cc_start: 0.5328 (tpp) cc_final: 0.5015 (tpt) REVERT: G 64 MET cc_start: 0.8955 (mmm) cc_final: 0.8739 (mmp) REVERT: G 182 ARG cc_start: 0.7616 (ttp80) cc_final: 0.7049 (ttp80) REVERT: G 300 MET cc_start: 0.8243 (mtt) cc_final: 0.8019 (ttm) REVERT: H 319 MET cc_start: 0.6923 (tpp) cc_final: 0.5415 (tpp) REVERT: I 120 MET cc_start: 0.6398 (tpp) cc_final: 0.6192 (tmm) REVERT: I 193 ARG cc_start: 0.6411 (ptp-170) cc_final: 0.6209 (ptp-170) outliers start: 88 outliers final: 56 residues processed: 902 average time/residue: 0.7228 time to fit residues: 1101.0582 Evaluate side-chains 811 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 751 time to evaluate : 6.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 856 GLN Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 237 GLU Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 588 LEU Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 693 LEU Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 7 residue 115 GLU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 675 MET Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 8 residue 151 LEU Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 370 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 464 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 696 optimal weight: 4.9990 chunk 569 optimal weight: 0.3980 chunk 230 optimal weight: 10.0000 chunk 837 optimal weight: 8.9990 chunk 905 optimal weight: 2.9990 chunk 746 optimal weight: 0.0370 chunk 830 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 672 optimal weight: 0.3980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 432 ASN 3 151 HIS 3 670 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 20 ASN 5 524 ASN 5 539 ASN 5 560 HIS 5 636 ASN 8 64 HIS ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 856 GLN C 46 GLN C 417 GLN C 722 ASN E 499 GLN E 524 ASN E 539 ASN ** G 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN H 125 HIS I 273 GLN I 339 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 75620 Z= 0.185 Angle : 0.510 13.847 102294 Z= 0.260 Chirality : 0.042 0.210 11714 Planarity : 0.004 0.059 13096 Dihedral : 8.201 166.819 10434 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.14 % Allowed : 9.16 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.09), residues: 9146 helix: 0.96 (0.09), residues: 3610 sheet: -0.84 (0.12), residues: 1630 loop : -0.35 (0.10), residues: 3906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 6 356 HIS 0.010 0.001 HIS F 653 PHE 0.017 0.001 PHE H 65 TYR 0.027 0.001 TYR 8 426 ARG 0.006 0.000 ARG 6 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 812 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 237 MET cc_start: 0.7902 (mtm) cc_final: 0.7688 (mtp) REVERT: 2 764 MET cc_start: 0.7200 (mtm) cc_final: 0.6940 (mtm) REVERT: 2 835 ASP cc_start: 0.7793 (m-30) cc_final: 0.7486 (m-30) REVERT: 3 281 ASP cc_start: 0.6850 (t0) cc_final: 0.6641 (t0) REVERT: 3 557 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7388 (tpp80) REVERT: 5 153 SER cc_start: 0.8793 (p) cc_final: 0.8546 (p) REVERT: 5 393 MET cc_start: 0.8534 (mmp) cc_final: 0.8150 (mmp) REVERT: 5 543 GLN cc_start: 0.7380 (tt0) cc_final: 0.7141 (tt0) REVERT: 5 583 MET cc_start: 0.4372 (mtt) cc_final: 0.3971 (ttm) REVERT: 6 117 GLN cc_start: 0.7844 (mt0) cc_final: 0.7595 (mt0) REVERT: 6 656 MET cc_start: 0.7705 (mtt) cc_final: 0.7348 (mtt) REVERT: 6 726 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7015 (mm-30) REVERT: 6 801 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6638 (mt-10) REVERT: 7 186 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: 7 300 MET cc_start: 0.8110 (mtt) cc_final: 0.7792 (ttm) REVERT: 7 330 SER cc_start: 0.8769 (p) cc_final: 0.8374 (m) REVERT: 7 621 MET cc_start: 0.7435 (mtm) cc_final: 0.7217 (mtp) REVERT: 8 146 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7849 (mm-30) REVERT: 9 531 MET cc_start: 0.8684 (mmm) cc_final: 0.8289 (mmm) REVERT: 9 535 LYS cc_start: 0.5134 (ptmt) cc_final: 0.4563 (mmmt) REVERT: B 653 ASN cc_start: 0.7815 (t0) cc_final: 0.7583 (t0) REVERT: B 827 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6329 (tt0) REVERT: C 703 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7739 (mt-10) REVERT: D 178 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7735 (mmm-85) REVERT: D 273 ASP cc_start: 0.7870 (m-30) cc_final: 0.7473 (m-30) REVERT: D 408 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7929 (p0) REVERT: D 799 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7000 (mt-10) REVERT: E 352 GLU cc_start: 0.5781 (tp30) cc_final: 0.5396 (mm-30) REVERT: E 514 ASN cc_start: 0.7859 (m-40) cc_final: 0.7445 (m-40) REVERT: F 313 MET cc_start: 0.5277 (tpp) cc_final: 0.4978 (tpt) REVERT: F 772 TYR cc_start: 0.7585 (t80) cc_final: 0.7319 (t80) REVERT: G 64 MET cc_start: 0.8897 (mmm) cc_final: 0.8679 (mmp) REVERT: G 300 MET cc_start: 0.8271 (mtt) cc_final: 0.8063 (ttm) outliers start: 94 outliers final: 64 residues processed: 868 average time/residue: 0.7141 time to fit residues: 1056.5467 Evaluate side-chains 823 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 756 time to evaluate : 6.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 856 GLN Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 588 LEU Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 640 SER Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 726 GLU Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 8 residue 151 LEU Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 9 residue 364 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 856 GLN Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 370 THR Chi-restraints excluded: chain I residue 510 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 827 optimal weight: 0.3980 chunk 629 optimal weight: 5.9990 chunk 434 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 399 optimal weight: 9.9990 chunk 562 optimal weight: 0.0470 chunk 840 optimal weight: 8.9990 chunk 890 optimal weight: 7.9990 chunk 439 optimal weight: 5.9990 chunk 796 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 overall best weight: 3.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 454 ASN 3 46 GLN 3 670 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 716 ASN 5 524 ASN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 9 GLN ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 367 ASN 8 401 GLN 9 510 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 260 GLN D 685 ASN E 524 ASN E 539 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS I 273 GLN ** I 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 75620 Z= 0.405 Angle : 0.611 10.792 102294 Z= 0.313 Chirality : 0.046 0.200 11714 Planarity : 0.005 0.060 13096 Dihedral : 8.316 163.840 10434 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.95 % Allowed : 10.92 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.09), residues: 9146 helix: 0.70 (0.09), residues: 3602 sheet: -1.01 (0.12), residues: 1672 loop : -0.44 (0.10), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 275 HIS 0.012 0.001 HIS F 653 PHE 0.033 0.002 PHE 2 271 TYR 0.031 0.002 TYR D 306 ARG 0.012 0.001 ARG I 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 800 time to evaluate : 6.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 581 ARG cc_start: 0.7303 (ptt90) cc_final: 0.7044 (ptm-80) REVERT: 2 764 MET cc_start: 0.7366 (mtm) cc_final: 0.7043 (mtm) REVERT: 2 835 ASP cc_start: 0.7849 (m-30) cc_final: 0.7544 (m-30) REVERT: 3 151 HIS cc_start: 0.7016 (m170) cc_final: 0.6794 (m90) REVERT: 3 320 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8580 (pp) REVERT: 4 732 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6916 (ttmt) REVERT: 5 153 SER cc_start: 0.9054 (p) cc_final: 0.8814 (p) REVERT: 5 543 GLN cc_start: 0.7408 (tt0) cc_final: 0.7178 (tt0) REVERT: 6 117 GLN cc_start: 0.7814 (mt0) cc_final: 0.7524 (mt0) REVERT: 6 156 GLN cc_start: 0.7776 (tp40) cc_final: 0.7529 (mm110) REVERT: 6 656 MET cc_start: 0.8153 (mtt) cc_final: 0.7725 (mtt) REVERT: 6 801 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6681 (mt-10) REVERT: 6 835 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8448 (mp) REVERT: 7 74 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: 7 186 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: 8 146 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7841 (mm-30) REVERT: 9 531 MET cc_start: 0.8613 (mmm) cc_final: 0.8124 (mmm) REVERT: 9 535 LYS cc_start: 0.5576 (ptmt) cc_final: 0.4873 (mmmt) REVERT: B 227 TYR cc_start: 0.6722 (m-10) cc_final: 0.6521 (m-10) REVERT: B 612 MET cc_start: 0.8366 (mtm) cc_final: 0.8115 (mtm) REVERT: B 827 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6405 (tm-30) REVERT: C 320 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 624 LYS cc_start: 0.7024 (mmpt) cc_final: 0.6822 (mmtt) REVERT: C 703 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7870 (mt-10) REVERT: C 735 PHE cc_start: 0.8660 (t80) cc_final: 0.8448 (t80) REVERT: D 178 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.7800 (mmm160) REVERT: D 273 ASP cc_start: 0.7920 (m-30) cc_final: 0.7493 (m-30) REVERT: D 408 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7954 (p0) REVERT: D 612 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8338 (mmtm) REVERT: D 799 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7200 (mt-10) REVERT: E 132 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7899 (pp) REVERT: E 352 GLU cc_start: 0.6023 (tp30) cc_final: 0.5675 (mm-30) REVERT: E 514 ASN cc_start: 0.8057 (m-40) cc_final: 0.7709 (m-40) REVERT: F 519 MET cc_start: 0.8469 (mtp) cc_final: 0.8222 (mtp) REVERT: F 726 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: G 183 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: H 56 LYS cc_start: 0.7060 (tttm) cc_final: 0.6858 (tttm) REVERT: H 97 MET cc_start: 0.8594 (ptp) cc_final: 0.8187 (ptm) REVERT: H 160 ILE cc_start: 0.8327 (mt) cc_final: 0.8116 (mt) REVERT: I 120 MET cc_start: 0.6359 (tmm) cc_final: 0.6153 (tmm) outliers start: 161 outliers final: 96 residues processed: 909 average time/residue: 0.7289 time to fit residues: 1124.8805 Evaluate side-chains 845 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 739 time to evaluate : 6.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 273 LEU Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 805 ILE Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 343 THR Chi-restraints excluded: chain 3 residue 588 LEU Chi-restraints excluded: chain 4 residue 218 ASN Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 678 ILE Chi-restraints excluded: chain 4 residue 732 LYS Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 348 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 693 LEU Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 74 GLU Chi-restraints excluded: chain 7 residue 151 GLU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 428 LEU Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 9 residue 364 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 640 SER Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 326 LYS Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 396 ASP Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 269 GLU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 367 ILE Chi-restraints excluded: chain I residue 370 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 741 optimal weight: 2.9990 chunk 505 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 662 optimal weight: 4.9990 chunk 367 optimal weight: 0.7980 chunk 759 optimal weight: 0.0570 chunk 615 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 454 optimal weight: 4.9990 chunk 799 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 2 658 ASN 3 151 HIS ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 646 HIS 5 524 ASN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS D 184 ASN D 366 GLN E 20 ASN E 524 ASN F 117 GLN ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 HIS I 286 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 75620 Z= 0.167 Angle : 0.498 10.223 102294 Z= 0.254 Chirality : 0.041 0.182 11714 Planarity : 0.004 0.058 13096 Dihedral : 7.982 154.289 10434 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.64 % Allowed : 12.25 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.09), residues: 9146 helix: 1.02 (0.09), residues: 3628 sheet: -0.79 (0.12), residues: 1652 loop : -0.35 (0.10), residues: 3866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 111 HIS 0.012 0.001 HIS F 653 PHE 0.017 0.001 PHE 2 271 TYR 0.034 0.001 TYR 8 426 ARG 0.009 0.000 ARG 6 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 826 time to evaluate : 6.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 237 MET cc_start: 0.7773 (mtm) cc_final: 0.7558 (mtp) REVERT: 2 835 ASP cc_start: 0.7850 (m-30) cc_final: 0.7559 (m-30) REVERT: 3 151 HIS cc_start: 0.7060 (m-70) cc_final: 0.6813 (m90) REVERT: 3 559 ARG cc_start: 0.7800 (ttm110) cc_final: 0.7141 (mtm110) REVERT: 4 273 ASP cc_start: 0.8003 (m-30) cc_final: 0.7610 (m-30) REVERT: 4 844 LYS cc_start: 0.7389 (mtpp) cc_final: 0.6886 (mtmm) REVERT: 5 153 SER cc_start: 0.8863 (p) cc_final: 0.8645 (p) REVERT: 5 539 ASN cc_start: 0.7026 (t160) cc_final: 0.6478 (t0) REVERT: 5 543 GLN cc_start: 0.7467 (tt0) cc_final: 0.7215 (tt0) REVERT: 5 552 MET cc_start: 0.8353 (mtm) cc_final: 0.8135 (mtm) REVERT: 5 583 MET cc_start: 0.4237 (mtt) cc_final: 0.3883 (mtm) REVERT: 6 117 GLN cc_start: 0.7856 (mt0) cc_final: 0.7543 (mt0) REVERT: 6 156 GLN cc_start: 0.7726 (tp40) cc_final: 0.7502 (mm110) REVERT: 6 656 MET cc_start: 0.7934 (mtt) cc_final: 0.7424 (mtt) REVERT: 6 835 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8342 (mp) REVERT: 7 183 GLU cc_start: 0.7565 (tt0) cc_final: 0.7239 (tt0) REVERT: 7 186 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: 7 515 LEU cc_start: 0.8952 (tt) cc_final: 0.8732 (tp) REVERT: 7 621 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7388 (mtm) REVERT: 8 146 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7879 (mm-30) REVERT: 9 531 MET cc_start: 0.8635 (mmm) cc_final: 0.8233 (mmm) REVERT: 9 535 LYS cc_start: 0.5466 (ptmt) cc_final: 0.4928 (mmmt) REVERT: B 227 TYR cc_start: 0.6673 (m-10) cc_final: 0.6428 (m-10) REVERT: B 827 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6461 (tm-30) REVERT: C 320 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8662 (pp) REVERT: C 375 ASP cc_start: 0.7290 (m-30) cc_final: 0.7040 (m-30) REVERT: C 703 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 273 ASP cc_start: 0.7873 (m-30) cc_final: 0.7389 (m-30) REVERT: D 408 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7870 (p0) REVERT: D 493 ASN cc_start: 0.8585 (p0) cc_final: 0.8243 (p0) REVERT: D 612 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8157 (mmtm) REVERT: D 718 ARG cc_start: 0.7780 (tpt-90) cc_final: 0.7167 (ttm110) REVERT: D 799 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7088 (mt-10) REVERT: E 352 GLU cc_start: 0.5842 (tp30) cc_final: 0.5466 (mm-30) REVERT: E 514 ASN cc_start: 0.7915 (m-40) cc_final: 0.7548 (m-40) REVERT: F 726 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: G 152 ARG cc_start: 0.7325 (tpt-90) cc_final: 0.7027 (tpt-90) REVERT: G 183 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: G 187 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: G 350 ASP cc_start: 0.8741 (m-30) cc_final: 0.8514 (m-30) REVERT: H 56 LYS cc_start: 0.6981 (tttm) cc_final: 0.6773 (tttm) REVERT: H 125 HIS cc_start: 0.8157 (p-80) cc_final: 0.7838 (p90) REVERT: H 190 MET cc_start: 0.8315 (pmm) cc_final: 0.8106 (pmm) REVERT: I 120 MET cc_start: 0.6316 (tmm) cc_final: 0.5900 (tmm) outliers start: 135 outliers final: 86 residues processed: 909 average time/residue: 0.7082 time to fit residues: 1094.7028 Evaluate side-chains 866 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 772 time to evaluate : 6.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain B residue 241 SER Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 299 optimal weight: 9.9990 chunk 801 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 522 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 891 optimal weight: 40.0000 chunk 739 optimal weight: 2.9990 chunk 412 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 294 optimal weight: 0.7980 chunk 467 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 268 ASN 9 181 ASN 9 286 GLN ** 9 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 268 ASN I 181 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 75620 Z= 0.233 Angle : 0.514 9.454 102294 Z= 0.262 Chirality : 0.042 0.157 11714 Planarity : 0.004 0.056 13096 Dihedral : 7.944 154.449 10434 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.94 % Allowed : 12.70 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 9146 helix: 1.05 (0.09), residues: 3624 sheet: -0.85 (0.12), residues: 1668 loop : -0.33 (0.10), residues: 3854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 356 HIS 0.012 0.001 HIS F 653 PHE 0.021 0.001 PHE 2 271 TYR 0.031 0.001 TYR 8 426 ARG 0.011 0.000 ARG 6 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 799 time to evaluate : 6.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 237 MET cc_start: 0.7813 (mtm) cc_final: 0.7580 (mtp) REVERT: 2 835 ASP cc_start: 0.7846 (m-30) cc_final: 0.7551 (m-30) REVERT: 3 151 HIS cc_start: 0.6995 (m-70) cc_final: 0.6756 (m90) REVERT: 3 282 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8427 (mt) REVERT: 3 320 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8490 (pp) REVERT: 3 559 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7125 (mtm110) REVERT: 4 273 ASP cc_start: 0.8039 (m-30) cc_final: 0.7746 (m-30) REVERT: 4 445 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8184 (mtm110) REVERT: 4 836 TYR cc_start: 0.7783 (p90) cc_final: 0.7440 (p90) REVERT: 5 153 SER cc_start: 0.8868 (p) cc_final: 0.8645 (p) REVERT: 5 539 ASN cc_start: 0.7041 (t160) cc_final: 0.6461 (t0) REVERT: 5 543 GLN cc_start: 0.7375 (tt0) cc_final: 0.7110 (tt0) REVERT: 5 552 MET cc_start: 0.8360 (mtm) cc_final: 0.8151 (mtm) REVERT: 6 117 GLN cc_start: 0.7860 (mt0) cc_final: 0.7562 (mt0) REVERT: 6 143 MET cc_start: 0.8584 (ptm) cc_final: 0.8274 (ptm) REVERT: 6 156 GLN cc_start: 0.7731 (tp40) cc_final: 0.7503 (mm110) REVERT: 6 656 MET cc_start: 0.7987 (mtt) cc_final: 0.7434 (mtt) REVERT: 6 835 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8386 (mp) REVERT: 7 186 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: 7 515 LEU cc_start: 0.8997 (tt) cc_final: 0.8771 (tp) REVERT: 7 621 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: 8 146 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7907 (mm-30) REVERT: 9 120 MET cc_start: 0.4736 (tpp) cc_final: 0.3764 (tmm) REVERT: 9 531 MET cc_start: 0.8607 (mmm) cc_final: 0.8231 (mmm) REVERT: 9 535 LYS cc_start: 0.5570 (ptmt) cc_final: 0.5031 (mmmt) REVERT: B 262 LYS cc_start: 0.7906 (tppt) cc_final: 0.7438 (mmtp) REVERT: B 827 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6578 (tm-30) REVERT: C 264 MET cc_start: 0.8182 (mtp) cc_final: 0.7910 (mtp) REVERT: C 320 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8708 (pp) REVERT: C 375 ASP cc_start: 0.7284 (m-30) cc_final: 0.7035 (m-30) REVERT: C 670 GLN cc_start: 0.8038 (mm110) cc_final: 0.7743 (mm-40) REVERT: D 178 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7473 (mmm160) REVERT: D 273 ASP cc_start: 0.7927 (m-30) cc_final: 0.7462 (m-30) REVERT: D 408 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7883 (p0) REVERT: D 493 ASN cc_start: 0.8701 (p0) cc_final: 0.8394 (p0) REVERT: D 612 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8233 (mmtm) REVERT: D 718 ARG cc_start: 0.7793 (tpt-90) cc_final: 0.7219 (ttm110) REVERT: D 799 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7040 (mt-10) REVERT: E 132 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7884 (pp) REVERT: E 514 ASN cc_start: 0.7964 (m-40) cc_final: 0.7576 (m-40) REVERT: F 726 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: G 152 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.7079 (tpt-90) REVERT: G 183 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: G 350 ASP cc_start: 0.8769 (m-30) cc_final: 0.8505 (m-30) REVERT: H 125 HIS cc_start: 0.8211 (p-80) cc_final: 0.7922 (p90) REVERT: I 120 MET cc_start: 0.6265 (tmm) cc_final: 0.5770 (tmm) REVERT: I 181 ASN cc_start: 0.4077 (OUTLIER) cc_final: 0.3303 (m110) outliers start: 160 outliers final: 109 residues processed: 906 average time/residue: 0.7212 time to fit residues: 1105.2359 Evaluate side-chains 897 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 776 time to evaluate : 6.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 282 LEU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 588 LEU Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 445 ARG Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 678 ILE Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 69 ILE Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 693 LEU Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 259 VAL Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 9 residue 364 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 664 LYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 701 MET Chi-restraints excluded: chain F residue 726 GLU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 259 VAL Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 859 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 507 optimal weight: 0.1980 chunk 650 optimal weight: 0.9980 chunk 504 optimal weight: 6.9990 chunk 750 optimal weight: 5.9990 chunk 497 optimal weight: 5.9990 chunk 887 optimal weight: 5.9990 chunk 555 optimal weight: 0.9990 chunk 541 optimal weight: 2.9990 chunk 409 optimal weight: 0.3980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 3 417 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 499 GLN 5 524 ASN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** I 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 75620 Z= 0.163 Angle : 0.489 10.476 102294 Z= 0.249 Chirality : 0.041 0.186 11714 Planarity : 0.004 0.055 13096 Dihedral : 7.812 151.786 10434 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 13.05 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 9146 helix: 1.22 (0.09), residues: 3606 sheet: -0.79 (0.12), residues: 1698 loop : -0.26 (0.10), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 6 356 HIS 0.011 0.001 HIS F 653 PHE 0.017 0.001 PHE 8 317 TYR 0.033 0.001 TYR 8 426 ARG 0.012 0.000 ARG 6 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 813 time to evaluate : 6.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 237 MET cc_start: 0.7725 (mtm) cc_final: 0.7505 (mtp) REVERT: 2 764 MET cc_start: 0.7384 (mtm) cc_final: 0.7172 (ptp) REVERT: 2 835 ASP cc_start: 0.7843 (m-30) cc_final: 0.7556 (m-30) REVERT: 3 282 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8304 (mt) REVERT: 3 320 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8460 (pp) REVERT: 3 490 MET cc_start: 0.9031 (mtp) cc_final: 0.8767 (mtt) REVERT: 3 559 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7107 (mtm110) REVERT: 4 273 ASP cc_start: 0.7993 (m-30) cc_final: 0.7691 (m-30) REVERT: 4 445 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8172 (mtm110) REVERT: 4 836 TYR cc_start: 0.7760 (p90) cc_final: 0.7425 (p90) REVERT: 4 844 LYS cc_start: 0.7460 (mtpp) cc_final: 0.7115 (mtmm) REVERT: 5 153 SER cc_start: 0.8783 (p) cc_final: 0.8557 (p) REVERT: 5 539 ASN cc_start: 0.7008 (t160) cc_final: 0.6440 (t0) REVERT: 5 543 GLN cc_start: 0.7421 (tt0) cc_final: 0.7082 (tt0) REVERT: 5 583 MET cc_start: 0.4330 (mtt) cc_final: 0.3955 (mtm) REVERT: 6 117 GLN cc_start: 0.7838 (mt0) cc_final: 0.7539 (mt0) REVERT: 6 143 MET cc_start: 0.8571 (ptm) cc_final: 0.8270 (ptm) REVERT: 6 835 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8360 (mp) REVERT: 7 186 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: 7 330 SER cc_start: 0.8861 (p) cc_final: 0.8465 (m) REVERT: 7 515 LEU cc_start: 0.8946 (tt) cc_final: 0.8733 (tp) REVERT: 7 621 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7413 (mtm) REVERT: 8 146 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7857 (mm-30) REVERT: 9 531 MET cc_start: 0.8622 (mmm) cc_final: 0.8265 (mmm) REVERT: 9 535 LYS cc_start: 0.5619 (ptmt) cc_final: 0.5126 (mmmt) REVERT: B 262 LYS cc_start: 0.7892 (tppt) cc_final: 0.7428 (mmtp) REVERT: B 272 ASP cc_start: 0.6923 (m-30) cc_final: 0.6538 (m-30) REVERT: B 827 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6640 (tm-30) REVERT: C 320 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8680 (pp) REVERT: C 375 ASP cc_start: 0.7252 (m-30) cc_final: 0.7023 (m-30) REVERT: C 670 GLN cc_start: 0.8012 (mm110) cc_final: 0.7741 (mm-40) REVERT: D 273 ASP cc_start: 0.7908 (m-30) cc_final: 0.7440 (m-30) REVERT: D 408 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7863 (p0) REVERT: D 493 ASN cc_start: 0.8669 (p0) cc_final: 0.8316 (p0) REVERT: D 612 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8168 (mmtm) REVERT: D 718 ARG cc_start: 0.7773 (tpt-90) cc_final: 0.7263 (ttm110) REVERT: D 799 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7017 (mt-10) REVERT: E 132 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7808 (pp) REVERT: E 514 ASN cc_start: 0.7944 (m-40) cc_final: 0.7538 (m-40) REVERT: G 152 ARG cc_start: 0.7369 (tpt-90) cc_final: 0.7075 (tpt-90) REVERT: G 183 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6739 (tt0) REVERT: G 187 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: H 125 HIS cc_start: 0.8320 (p-80) cc_final: 0.7945 (p90) REVERT: H 126 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7627 (mm-30) REVERT: I 120 MET cc_start: 0.6409 (tmm) cc_final: 0.5825 (tmm) outliers start: 153 outliers final: 105 residues processed: 909 average time/residue: 0.7130 time to fit residues: 1101.4288 Evaluate side-chains 900 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 784 time to evaluate : 6.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 613 ASN Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 805 ILE Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 282 LEU Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 445 ARG Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 678 ILE Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 487 ASP Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 132 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 498 MET Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 625 GLN Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 701 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 324 ASP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Chi-restraints excluded: chain I residue 510 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 549 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 chunk 530 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 564 optimal weight: 4.9990 chunk 604 optimal weight: 2.9990 chunk 438 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 697 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 3 151 HIS 3 417 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 499 GLN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 673 GLN D 613 GLN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN H 125 HIS I 181 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 75620 Z= 0.148 Angle : 0.480 10.566 102294 Z= 0.243 Chirality : 0.040 0.148 11714 Planarity : 0.004 0.054 13096 Dihedral : 7.686 150.316 10432 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 13.39 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 9146 helix: 1.34 (0.09), residues: 3610 sheet: -0.75 (0.12), residues: 1684 loop : -0.21 (0.10), residues: 3852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 356 HIS 0.010 0.001 HIS F 653 PHE 0.024 0.001 PHE 9 210 TYR 0.030 0.001 TYR 8 426 ARG 0.014 0.000 ARG 6 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 828 time to evaluate : 6.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 558 LYS cc_start: 0.8170 (mttt) cc_final: 0.7899 (mttm) REVERT: 2 835 ASP cc_start: 0.7882 (m-30) cc_final: 0.7603 (m-30) REVERT: 3 282 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8309 (mt) REVERT: 3 320 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8454 (pp) REVERT: 3 559 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7073 (mtm110) REVERT: 4 273 ASP cc_start: 0.7966 (m-30) cc_final: 0.7673 (m-30) REVERT: 4 445 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8169 (mtm110) REVERT: 4 836 TYR cc_start: 0.7789 (p90) cc_final: 0.7439 (p90) REVERT: 4 844 LYS cc_start: 0.7512 (mtpp) cc_final: 0.7180 (mtmm) REVERT: 5 153 SER cc_start: 0.8725 (p) cc_final: 0.8513 (p) REVERT: 5 539 ASN cc_start: 0.6951 (t160) cc_final: 0.6435 (t0) REVERT: 5 543 GLN cc_start: 0.7371 (tt0) cc_final: 0.7021 (tt0) REVERT: 5 583 MET cc_start: 0.4297 (mtt) cc_final: 0.3935 (mtm) REVERT: 6 117 GLN cc_start: 0.7831 (mt0) cc_final: 0.7531 (mt0) REVERT: 6 143 MET cc_start: 0.8567 (ptm) cc_final: 0.8279 (ptm) REVERT: 6 835 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8322 (mp) REVERT: 7 186 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: 7 330 SER cc_start: 0.8805 (p) cc_final: 0.8438 (m) REVERT: 7 621 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: 8 146 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7848 (mm-30) REVERT: 8 293 CYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7025 (t) REVERT: 9 120 MET cc_start: 0.3932 (tpp) cc_final: 0.2724 (tmm) REVERT: 9 146 LYS cc_start: 0.5396 (ptpt) cc_final: 0.4731 (mtpt) REVERT: 9 531 MET cc_start: 0.8591 (mmm) cc_final: 0.8301 (mmm) REVERT: 9 535 LYS cc_start: 0.5719 (ptmt) cc_final: 0.5232 (mmmt) REVERT: B 262 LYS cc_start: 0.7907 (tppt) cc_final: 0.7435 (mmtp) REVERT: B 827 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6641 (tm-30) REVERT: C 320 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8653 (pp) REVERT: C 375 ASP cc_start: 0.7128 (m-30) cc_final: 0.6848 (m-30) REVERT: C 670 GLN cc_start: 0.8032 (mm110) cc_final: 0.7704 (mm-40) REVERT: D 184 ASN cc_start: 0.7767 (m-40) cc_final: 0.7534 (m-40) REVERT: D 273 ASP cc_start: 0.7902 (m-30) cc_final: 0.7431 (m-30) REVERT: D 408 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7860 (p0) REVERT: D 462 ASP cc_start: 0.8272 (m-30) cc_final: 0.7991 (t0) REVERT: D 493 ASN cc_start: 0.8633 (p0) cc_final: 0.8267 (p0) REVERT: D 718 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7286 (ttm110) REVERT: D 799 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6926 (mt-10) REVERT: E 132 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7821 (pp) REVERT: E 514 ASN cc_start: 0.7937 (m-40) cc_final: 0.7534 (m-40) REVERT: F 519 MET cc_start: 0.8391 (mtp) cc_final: 0.8135 (mtp) REVERT: G 152 ARG cc_start: 0.7376 (tpt-90) cc_final: 0.7098 (tpt-90) REVERT: G 183 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6650 (tt0) REVERT: G 187 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.7084 (m-30) REVERT: I 120 MET cc_start: 0.6367 (tmm) cc_final: 0.5725 (tmm) REVERT: I 181 ASN cc_start: 0.4232 (OUTLIER) cc_final: 0.3565 (m-40) outliers start: 143 outliers final: 111 residues processed: 924 average time/residue: 0.7454 time to fit residues: 1173.9607 Evaluate side-chains 913 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 789 time to evaluate : 6.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 613 ASN Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 282 LEU Chi-restraints excluded: chain 3 residue 300 SER Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 445 ARG Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 678 ILE Chi-restraints excluded: chain 4 residue 777 MET Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 487 ASP Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 132 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 151 GLU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 498 MET Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 625 GLN Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 293 CYS Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 9 residue 364 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 701 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 181 ASN Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Chi-restraints excluded: chain I residue 510 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 807 optimal weight: 0.0070 chunk 850 optimal weight: 8.9990 chunk 775 optimal weight: 2.9990 chunk 827 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 649 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 747 optimal weight: 9.9990 chunk 782 optimal weight: 0.9990 chunk 824 optimal weight: 5.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 3 151 HIS ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 524 ASN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 673 GLN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 GLN D 613 GLN E 499 GLN E 539 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 ASN I 339 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 75620 Z= 0.287 Angle : 0.542 11.238 102294 Z= 0.275 Chirality : 0.043 0.202 11714 Planarity : 0.004 0.063 13096 Dihedral : 7.825 151.740 10432 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.92 % Allowed : 13.44 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 9146 helix: 1.17 (0.09), residues: 3614 sheet: -0.79 (0.12), residues: 1684 loop : -0.28 (0.10), residues: 3848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 356 HIS 0.012 0.001 HIS F 653 PHE 0.024 0.001 PHE 2 271 TYR 0.029 0.001 TYR 8 426 ARG 0.014 0.000 ARG F 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 794 time to evaluate : 6.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 237 MET cc_start: 0.7715 (mtm) cc_final: 0.7507 (mtp) REVERT: 2 558 LYS cc_start: 0.8166 (mttt) cc_final: 0.7863 (mttm) REVERT: 2 835 ASP cc_start: 0.7844 (m-30) cc_final: 0.7559 (m-30) REVERT: 3 151 HIS cc_start: 0.7020 (m-70) cc_final: 0.6801 (m90) REVERT: 3 282 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8462 (mt) REVERT: 3 320 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8498 (pp) REVERT: 3 559 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7086 (mtm110) REVERT: 4 273 ASP cc_start: 0.8030 (m-30) cc_final: 0.7734 (m-30) REVERT: 4 401 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7570 (mm-30) REVERT: 4 445 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8166 (mtm110) REVERT: 4 836 TYR cc_start: 0.7797 (p90) cc_final: 0.7490 (p90) REVERT: 4 844 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7132 (mtmm) REVERT: 5 153 SER cc_start: 0.8916 (p) cc_final: 0.8683 (p) REVERT: 5 539 ASN cc_start: 0.7050 (t160) cc_final: 0.6456 (t0) REVERT: 5 543 GLN cc_start: 0.7399 (tt0) cc_final: 0.7069 (tt0) REVERT: 6 117 GLN cc_start: 0.7802 (mt0) cc_final: 0.7486 (mt0) REVERT: 6 143 MET cc_start: 0.8574 (ptm) cc_final: 0.8277 (ptm) REVERT: 6 656 MET cc_start: 0.8053 (mtt) cc_final: 0.7589 (mtt) REVERT: 6 835 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8410 (mp) REVERT: 7 153 MET cc_start: 0.8109 (mtp) cc_final: 0.7826 (mtm) REVERT: 7 186 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: 7 621 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7450 (mtm) REVERT: 8 146 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7878 (mm-30) REVERT: 8 293 CYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7044 (t) REVERT: 9 120 MET cc_start: 0.3965 (tpp) cc_final: 0.2972 (tmm) REVERT: 9 144 MET cc_start: 0.7182 (mmt) cc_final: 0.6969 (tpp) REVERT: 9 146 LYS cc_start: 0.5426 (ptpt) cc_final: 0.4745 (mtpt) REVERT: 9 531 MET cc_start: 0.8588 (mmm) cc_final: 0.8231 (mmm) REVERT: 9 535 LYS cc_start: 0.5733 (ptmt) cc_final: 0.5167 (mmmt) REVERT: B 179 GLU cc_start: 0.5236 (mp0) cc_final: 0.4997 (mt-10) REVERT: B 262 LYS cc_start: 0.7982 (tppt) cc_final: 0.7525 (mmtp) REVERT: B 827 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6681 (tm-30) REVERT: C 320 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8710 (pp) REVERT: C 375 ASP cc_start: 0.7181 (m-30) cc_final: 0.6901 (m-30) REVERT: C 670 GLN cc_start: 0.8034 (mm110) cc_final: 0.7719 (mm-40) REVERT: D 273 ASP cc_start: 0.7942 (m-30) cc_final: 0.7482 (m-30) REVERT: D 408 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7923 (p0) REVERT: D 493 ASN cc_start: 0.8742 (p0) cc_final: 0.8412 (p0) REVERT: D 718 ARG cc_start: 0.7812 (tpt-90) cc_final: 0.7281 (ttm110) REVERT: D 799 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7076 (mt-10) REVERT: E 132 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7863 (pp) REVERT: F 801 GLU cc_start: 0.6934 (mp0) cc_final: 0.6602 (mp0) REVERT: G 152 ARG cc_start: 0.7436 (tpt-90) cc_final: 0.7144 (tpt-90) REVERT: G 183 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: I 120 MET cc_start: 0.6457 (tmm) cc_final: 0.5761 (tmm) outliers start: 158 outliers final: 124 residues processed: 895 average time/residue: 0.7079 time to fit residues: 1081.4850 Evaluate side-chains 902 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 767 time to evaluate : 6.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 217 GLU Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 613 ASN Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 784 ASP Chi-restraints excluded: chain 2 residue 805 ILE Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 160 SER Chi-restraints excluded: chain 3 residue 282 LEU Chi-restraints excluded: chain 3 residue 300 SER Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 445 ARG Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 678 ILE Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 458 MET Chi-restraints excluded: chain 5 residue 493 ILE Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 132 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 151 GLU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 220 ILE Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 498 MET Chi-restraints excluded: chain 7 residue 508 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 712 ASP Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 293 CYS Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 8 residue 466 THR Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 201 VAL Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain 9 residue 364 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 660 THR Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 855 ARG Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 424 ARG Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 701 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 396 ASP Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 45 SER Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 324 ASP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Chi-restraints excluded: chain I residue 510 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 543 optimal weight: 1.9990 chunk 874 optimal weight: 5.9990 chunk 533 optimal weight: 0.8980 chunk 414 optimal weight: 0.9990 chunk 608 optimal weight: 0.8980 chunk 917 optimal weight: 9.9990 chunk 844 optimal weight: 0.5980 chunk 730 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 564 optimal weight: 0.9990 chunk 448 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 3 417 GLN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 499 GLN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 673 GLN B 282 HIS D 613 GLN E 524 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 75620 Z= 0.139 Angle : 0.483 11.079 102294 Z= 0.245 Chirality : 0.040 0.152 11714 Planarity : 0.004 0.056 13096 Dihedral : 7.612 147.831 10432 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 13.89 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 9146 helix: 1.41 (0.09), residues: 3590 sheet: -0.68 (0.12), residues: 1652 loop : -0.22 (0.10), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 111 HIS 0.011 0.001 HIS F 653 PHE 0.021 0.001 PHE 8 317 TYR 0.028 0.001 TYR 8 426 ARG 0.016 0.000 ARG 9 534 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18292 Ramachandran restraints generated. 9146 Oldfield, 0 Emsley, 9146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 808 time to evaluate : 6.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 558 LYS cc_start: 0.8158 (mttt) cc_final: 0.7839 (mttm) REVERT: 2 835 ASP cc_start: 0.7882 (m-30) cc_final: 0.7625 (m-30) REVERT: 3 151 HIS cc_start: 0.7012 (m-70) cc_final: 0.6795 (m90) REVERT: 3 282 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8310 (mt) REVERT: 3 320 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8479 (pp) REVERT: 3 559 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7047 (mtm110) REVERT: 4 273 ASP cc_start: 0.7947 (m-30) cc_final: 0.7649 (m-30) REVERT: 4 836 TYR cc_start: 0.7783 (p90) cc_final: 0.7459 (p90) REVERT: 4 844 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7154 (mtmm) REVERT: 5 153 SER cc_start: 0.8721 (p) cc_final: 0.8504 (p) REVERT: 5 539 ASN cc_start: 0.6963 (t160) cc_final: 0.6445 (t0) REVERT: 5 543 GLN cc_start: 0.7384 (tt0) cc_final: 0.7076 (tt0) REVERT: 5 583 MET cc_start: 0.4252 (mtt) cc_final: 0.3915 (mtm) REVERT: 6 117 GLN cc_start: 0.7818 (mt0) cc_final: 0.7517 (mt0) REVERT: 6 143 MET cc_start: 0.8561 (ptm) cc_final: 0.8279 (ptm) REVERT: 6 835 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8331 (mp) REVERT: 7 153 MET cc_start: 0.8126 (mtp) cc_final: 0.7871 (mtm) REVERT: 7 186 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: 7 330 SER cc_start: 0.8797 (p) cc_final: 0.8422 (m) REVERT: 7 621 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7395 (mtm) REVERT: 8 146 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7808 (mm-30) REVERT: 8 293 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6938 (t) REVERT: 8 434 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7820 (tp30) REVERT: 9 120 MET cc_start: 0.3892 (tpp) cc_final: 0.3665 (mmp) REVERT: 9 146 LYS cc_start: 0.5412 (ptpt) cc_final: 0.4759 (mtpt) REVERT: 9 339 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7545 (mt0) REVERT: 9 531 MET cc_start: 0.8609 (mmm) cc_final: 0.8308 (mmm) REVERT: 9 535 LYS cc_start: 0.5708 (ptmt) cc_final: 0.5257 (mmmt) REVERT: B 262 LYS cc_start: 0.7958 (tppt) cc_final: 0.7501 (mmtt) REVERT: B 827 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6667 (tm-30) REVERT: C 320 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8641 (pp) REVERT: C 375 ASP cc_start: 0.7134 (m-30) cc_final: 0.6822 (m-30) REVERT: C 487 HIS cc_start: 0.7858 (m90) cc_final: 0.7607 (m90) REVERT: C 670 GLN cc_start: 0.8000 (mm110) cc_final: 0.7712 (mm-40) REVERT: D 184 ASN cc_start: 0.7741 (m-40) cc_final: 0.7502 (m-40) REVERT: D 273 ASP cc_start: 0.7862 (m-30) cc_final: 0.7385 (m-30) REVERT: D 408 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7865 (p0) REVERT: D 462 ASP cc_start: 0.8285 (m-30) cc_final: 0.7999 (t0) REVERT: D 493 ASN cc_start: 0.8621 (p0) cc_final: 0.8251 (p0) REVERT: D 718 ARG cc_start: 0.7800 (tpt-90) cc_final: 0.7260 (ttm110) REVERT: D 799 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6923 (mt-10) REVERT: F 132 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6542 (p) REVERT: G 152 ARG cc_start: 0.7392 (tpt-90) cc_final: 0.7126 (tpt-90) REVERT: I 120 MET cc_start: 0.6469 (tmm) cc_final: 0.5780 (tmm) outliers start: 124 outliers final: 99 residues processed: 883 average time/residue: 0.7518 time to fit residues: 1131.3459 Evaluate side-chains 886 residues out of total 8244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 778 time to evaluate : 6.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 226 VAL Chi-restraints excluded: chain 2 residue 241 SER Chi-restraints excluded: chain 2 residue 344 CYS Chi-restraints excluded: chain 2 residue 368 LYS Chi-restraints excluded: chain 2 residue 711 ASP Chi-restraints excluded: chain 2 residue 805 ILE Chi-restraints excluded: chain 2 residue 863 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 282 LEU Chi-restraints excluded: chain 3 residue 300 SER Chi-restraints excluded: chain 3 residue 320 LEU Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 336 VAL Chi-restraints excluded: chain 3 residue 519 VAL Chi-restraints excluded: chain 4 residue 289 LEU Chi-restraints excluded: chain 4 residue 341 ASP Chi-restraints excluded: chain 4 residue 359 GLU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 676 ASN Chi-restraints excluded: chain 4 residue 818 GLU Chi-restraints excluded: chain 4 residue 839 ASP Chi-restraints excluded: chain 5 residue 321 VAL Chi-restraints excluded: chain 5 residue 458 MET Chi-restraints excluded: chain 5 residue 487 ASP Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 132 VAL Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 318 VAL Chi-restraints excluded: chain 6 residue 400 VAL Chi-restraints excluded: chain 6 residue 662 SER Chi-restraints excluded: chain 6 residue 710 ASP Chi-restraints excluded: chain 6 residue 834 SER Chi-restraints excluded: chain 6 residue 835 ILE Chi-restraints excluded: chain 7 residue 127 LEU Chi-restraints excluded: chain 7 residue 186 GLU Chi-restraints excluded: chain 7 residue 189 THR Chi-restraints excluded: chain 7 residue 370 LEU Chi-restraints excluded: chain 7 residue 396 ASP Chi-restraints excluded: chain 7 residue 441 ASP Chi-restraints excluded: chain 7 residue 491 VAL Chi-restraints excluded: chain 7 residue 498 MET Chi-restraints excluded: chain 7 residue 503 THR Chi-restraints excluded: chain 7 residue 508 LEU Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain 7 residue 631 THR Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 8 residue 39 ILE Chi-restraints excluded: chain 8 residue 293 CYS Chi-restraints excluded: chain 8 residue 324 ASP Chi-restraints excluded: chain 8 residue 445 VAL Chi-restraints excluded: chain 9 residue 175 THR Chi-restraints excluded: chain 9 residue 188 THR Chi-restraints excluded: chain 9 residue 201 VAL Chi-restraints excluded: chain 9 residue 233 THR Chi-restraints excluded: chain 9 residue 243 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 344 CYS Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 839 ASP Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 424 ARG Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 701 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 396 ASP Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 441 ASP Chi-restraints excluded: chain G residue 443 ARG Chi-restraints excluded: chain G residue 504 ASP Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 674 GLU Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 300 ILE Chi-restraints excluded: chain H residue 324 ASP Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 391 VAL Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain I residue 233 THR Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 319 SER Chi-restraints excluded: chain I residue 370 THR Chi-restraints excluded: chain I residue 510 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 921 random chunks: chunk 580 optimal weight: 0.7980 chunk 778 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 673 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 731 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 751 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 3 417 GLN 4 184 ASN ** 4 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 499 GLN 5 560 HIS ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 673 GLN B 282 HIS D 613 GLN E 524 ASN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.159120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110279 restraints weight = 84483.327| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.00 r_work: 0.2880 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 75620 Z= 0.145 Angle : 0.480 10.858 102294 Z= 0.242 Chirality : 0.040 0.181 11714 Planarity : 0.004 0.061 13096 Dihedral : 7.525 147.357 10432 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 14.02 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 9146 helix: 1.47 (0.09), residues: 3594 sheet: -0.68 (0.12), residues: 1708 loop : -0.15 (0.10), residues: 3844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 356 HIS 0.009 0.001 HIS F 653 PHE 0.021 0.001 PHE 8 317 TYR 0.043 0.001 TYR 8 426 ARG 0.015 0.000 ARG 6 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18859.85 seconds wall clock time: 331 minutes 44.12 seconds (19904.12 seconds total)