Starting phenix.real_space_refine on Fri Mar 22 18:12:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/03_2024/7eeq_31080.pdb" } resolution = 3.96 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= 0.003 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 21726 2.51 5 N 5682 2.21 5 O 6786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 135": "NH1" <-> "NH2" Residue "1 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 240": "NH1" <-> "NH2" Residue "1 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 306": "NH1" <-> "NH2" Residue "1 ARG 333": "NH1" <-> "NH2" Residue "1 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 427": "NH1" <-> "NH2" Residue "1 ARG 440": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 68": "NH1" <-> "NH2" Residue "2 ARG 135": "NH1" <-> "NH2" Residue "2 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 240": "NH1" <-> "NH2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 306": "NH1" <-> "NH2" Residue "2 ARG 333": "NH1" <-> "NH2" Residue "2 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 427": "NH1" <-> "NH2" Residue "2 ARG 440": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 14": "NH1" <-> "NH2" Residue "3 ARG 68": "NH1" <-> "NH2" Residue "3 ARG 135": "NH1" <-> "NH2" Residue "3 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 240": "NH1" <-> "NH2" Residue "3 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 306": "NH1" <-> "NH2" Residue "3 ARG 333": "NH1" <-> "NH2" Residue "3 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 427": "NH1" <-> "NH2" Residue "3 ARG 440": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 68": "NH1" <-> "NH2" Residue "4 ARG 135": "NH1" <-> "NH2" Residue "4 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 240": "NH1" <-> "NH2" Residue "4 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 306": "NH1" <-> "NH2" Residue "4 ARG 333": "NH1" <-> "NH2" Residue "4 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 427": "NH1" <-> "NH2" Residue "4 ARG 440": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 ARG 68": "NH1" <-> "NH2" Residue "5 ARG 135": "NH1" <-> "NH2" Residue "5 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 240": "NH1" <-> "NH2" Residue "5 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 306": "NH1" <-> "NH2" Residue "5 ARG 333": "NH1" <-> "NH2" Residue "5 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 427": "NH1" <-> "NH2" Residue "5 ARG 440": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 68": "NH1" <-> "NH2" Residue "6 ARG 135": "NH1" <-> "NH2" Residue "6 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 240": "NH1" <-> "NH2" Residue "6 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 306": "NH1" <-> "NH2" Residue "6 ARG 333": "NH1" <-> "NH2" Residue "6 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 427": "NH1" <-> "NH2" Residue "6 ARG 440": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "H ARG 11": "NH1" <-> "NH2" Residue "I ARG 11": "NH1" <-> "NH2" Residue "J ARG 11": "NH1" <-> "NH2" Residue "K ARG 11": "NH1" <-> "NH2" Residue "L ARG 11": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "N ARG 11": "NH1" <-> "NH2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34260 Number of models: 1 Model: "" Number of chains: 24 Chain: "1" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "2" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "3" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "4" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "5" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "6" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3430 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain: "A" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "B" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "E" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "F" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "I" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "J" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "L" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "M" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "N" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "O" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "P" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "Q" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "R" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Time building chain proxies: 17.06, per 1000 atoms: 0.50 Number of scatterers: 34260 At special positions: 0 Unit cell: (181.327, 195.509, 107.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 6786 8.00 N 5682 7.00 C 21726 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.57 Conformation dependent library (CDL) restraints added in 6.1 seconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 118 sheets defined 2.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain '1' and resid 378 through 381 Processing helix chain '2' and resid 378 through 381 Processing helix chain '3' and resid 378 through 381 Processing helix chain '4' and resid 378 through 381 Processing helix chain '5' and resid 378 through 381 Processing helix chain '6' and resid 378 through 381 Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU F 98 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU L 98 " --> pdb=" O ILE L 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU M 98 " --> pdb=" O ILE M 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU N 98 " --> pdb=" O ILE N 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU O 98 " --> pdb=" O ILE O 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 99 removed outlier: 3.925A pdb=" N LEU P 98 " --> pdb=" O ILE P 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU Q 98 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 99 removed outlier: 3.926A pdb=" N LEU R 98 " --> pdb=" O ILE R 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 26 through 29 removed outlier: 10.143A pdb=" N VAL 1 35 " --> pdb=" O ASP 1 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 1 430 " --> pdb=" O VAL 1 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR 1 353 " --> pdb=" O SER 1 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 1 431 " --> pdb=" O ARG 1 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 1 351 " --> pdb=" O VAL 1 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 1 401 " --> pdb=" O LEU 1 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain '1' and resid 69 through 72 Processing sheet with id=AA4, first strand: chain '1' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 1 93 " --> pdb=" O ASN 1 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 1 110 " --> pdb=" O VAL 1 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 138 through 140 removed outlier: 3.660A pdb=" N TRP 1 147 " --> pdb=" O ALA 1 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 1 175 " --> pdb=" O PHE 1 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 222 through 223 Processing sheet with id=AA8, first strand: chain '1' and resid 239 through 240 Processing sheet with id=AA9, first strand: chain '1' and resid 264 through 270 Processing sheet with id=AB1, first strand: chain '1' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 1 337 " --> pdb=" O PHE 1 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 1 415 " --> pdb=" O SER 1 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 1 375 " --> pdb=" O ASP 1 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP 1 385 " --> pdb=" O PHE 1 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 1 377 " --> pdb=" O TRP 1 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 1 383 " --> pdb=" O TYR 1 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 1 345 " --> pdb=" O PHE 1 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 1 409 " --> pdb=" O THR 1 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 2 35 " --> pdb=" O ASP 2 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 2 430 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 2 353 " --> pdb=" O SER 2 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 2 431 " --> pdb=" O ARG 2 351 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG 2 351 " --> pdb=" O VAL 2 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 2 401 " --> pdb=" O LEU 2 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 47 through 48 Processing sheet with id=AB5, first strand: chain '2' and resid 69 through 72 Processing sheet with id=AB6, first strand: chain '2' and resid 93 through 96 removed outlier: 3.982A pdb=" N ARG 2 93 " --> pdb=" O ASN 2 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 2 110 " --> pdb=" O VAL 2 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '2' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 2 147 " --> pdb=" O ALA 2 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 2 175 " --> pdb=" O PHE 2 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 222 through 223 Processing sheet with id=AC1, first strand: chain '2' and resid 239 through 240 Processing sheet with id=AC2, first strand: chain '2' and resid 264 through 270 Processing sheet with id=AC3, first strand: chain '2' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 2 337 " --> pdb=" O PHE 2 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 2 415 " --> pdb=" O SER 2 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 2 375 " --> pdb=" O ASP 2 385 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP 2 385 " --> pdb=" O PHE 2 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 2 377 " --> pdb=" O TRP 2 383 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TRP 2 383 " --> pdb=" O TYR 2 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '2' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 2 345 " --> pdb=" O PHE 2 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 2 409 " --> pdb=" O THR 2 345 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 3 35 " --> pdb=" O ASP 3 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 3 430 " --> pdb=" O VAL 3 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 3 353 " --> pdb=" O SER 3 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 3 431 " --> pdb=" O ARG 3 351 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG 3 351 " --> pdb=" O VAL 3 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 3 401 " --> pdb=" O LEU 3 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '3' and resid 47 through 48 Processing sheet with id=AC7, first strand: chain '3' and resid 69 through 72 Processing sheet with id=AC8, first strand: chain '3' and resid 93 through 96 removed outlier: 3.982A pdb=" N ARG 3 93 " --> pdb=" O ASN 3 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 3 110 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 138 through 140 removed outlier: 3.662A pdb=" N TRP 3 147 " --> pdb=" O ALA 3 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '3' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 3 175 " --> pdb=" O PHE 3 186 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '3' and resid 222 through 223 Processing sheet with id=AD3, first strand: chain '3' and resid 239 through 240 Processing sheet with id=AD4, first strand: chain '3' and resid 264 through 270 Processing sheet with id=AD5, first strand: chain '3' and resid 332 through 338 removed outlier: 3.601A pdb=" N ALA 3 337 " --> pdb=" O PHE 3 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 3 415 " --> pdb=" O SER 3 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 3 375 " --> pdb=" O ASP 3 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 3 385 " --> pdb=" O PHE 3 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 3 377 " --> pdb=" O TRP 3 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 3 383 " --> pdb=" O TYR 3 377 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 3 345 " --> pdb=" O PHE 3 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 3 409 " --> pdb=" O THR 3 345 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '4' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 4 35 " --> pdb=" O ASP 4 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 4 430 " --> pdb=" O VAL 4 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 4 353 " --> pdb=" O SER 4 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 4 431 " --> pdb=" O ARG 4 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 4 351 " --> pdb=" O VAL 4 431 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 4 401 " --> pdb=" O LEU 4 352 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 47 through 48 Processing sheet with id=AD9, first strand: chain '4' and resid 69 through 72 Processing sheet with id=AE1, first strand: chain '4' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 4 93 " --> pdb=" O ASN 4 104 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 4 110 " --> pdb=" O VAL 4 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '4' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 4 147 " --> pdb=" O ALA 4 164 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '4' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 4 175 " --> pdb=" O PHE 4 186 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '4' and resid 222 through 223 Processing sheet with id=AE5, first strand: chain '4' and resid 239 through 240 Processing sheet with id=AE6, first strand: chain '4' and resid 264 through 270 Processing sheet with id=AE7, first strand: chain '4' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 4 337 " --> pdb=" O PHE 4 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 4 415 " --> pdb=" O SER 4 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 4 375 " --> pdb=" O ASP 4 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 4 385 " --> pdb=" O PHE 4 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 4 377 " --> pdb=" O TRP 4 383 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TRP 4 383 " --> pdb=" O TYR 4 377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '4' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 4 345 " --> pdb=" O PHE 4 409 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE 4 409 " --> pdb=" O THR 4 345 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '5' and resid 26 through 29 removed outlier: 10.144A pdb=" N VAL 5 35 " --> pdb=" O ASP 5 430 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASP 5 430 " --> pdb=" O VAL 5 35 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR 5 353 " --> pdb=" O SER 5 429 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL 5 431 " --> pdb=" O ARG 5 351 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG 5 351 " --> pdb=" O VAL 5 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL 5 401 " --> pdb=" O LEU 5 352 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '5' and resid 47 through 48 Processing sheet with id=AF2, first strand: chain '5' and resid 69 through 72 Processing sheet with id=AF3, first strand: chain '5' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 5 93 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR 5 110 " --> pdb=" O VAL 5 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '5' and resid 138 through 140 removed outlier: 3.662A pdb=" N TRP 5 147 " --> pdb=" O ALA 5 164 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '5' and resid 173 through 178 removed outlier: 3.544A pdb=" N ASP 5 175 " --> pdb=" O PHE 5 186 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '5' and resid 222 through 223 Processing sheet with id=AF7, first strand: chain '5' and resid 239 through 240 Processing sheet with id=AF8, first strand: chain '5' and resid 264 through 270 Processing sheet with id=AF9, first strand: chain '5' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 5 337 " --> pdb=" O PHE 5 416 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU 5 415 " --> pdb=" O SER 5 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 5 375 " --> pdb=" O ASP 5 385 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP 5 385 " --> pdb=" O PHE 5 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 5 377 " --> pdb=" O TRP 5 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 5 383 " --> pdb=" O TYR 5 377 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '5' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 5 345 " --> pdb=" O PHE 5 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 5 409 " --> pdb=" O THR 5 345 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '6' and resid 26 through 29 removed outlier: 10.143A pdb=" N VAL 6 35 " --> pdb=" O ASP 6 430 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP 6 430 " --> pdb=" O VAL 6 35 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR 6 353 " --> pdb=" O SER 6 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL 6 431 " --> pdb=" O ARG 6 351 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG 6 351 " --> pdb=" O VAL 6 431 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL 6 401 " --> pdb=" O LEU 6 352 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '6' and resid 47 through 48 Processing sheet with id=AG4, first strand: chain '6' and resid 69 through 72 Processing sheet with id=AG5, first strand: chain '6' and resid 93 through 96 removed outlier: 3.981A pdb=" N ARG 6 93 " --> pdb=" O ASN 6 104 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR 6 110 " --> pdb=" O VAL 6 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '6' and resid 138 through 140 removed outlier: 3.661A pdb=" N TRP 6 147 " --> pdb=" O ALA 6 164 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '6' and resid 173 through 178 removed outlier: 3.545A pdb=" N ASP 6 175 " --> pdb=" O PHE 6 186 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '6' and resid 222 through 223 Processing sheet with id=AG9, first strand: chain '6' and resid 239 through 240 Processing sheet with id=AH1, first strand: chain '6' and resid 264 through 270 Processing sheet with id=AH2, first strand: chain '6' and resid 332 through 338 removed outlier: 3.600A pdb=" N ALA 6 337 " --> pdb=" O PHE 6 416 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU 6 415 " --> pdb=" O SER 6 376 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE 6 375 " --> pdb=" O ASP 6 385 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP 6 385 " --> pdb=" O PHE 6 375 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR 6 377 " --> pdb=" O TRP 6 383 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TRP 6 383 " --> pdb=" O TYR 6 377 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '6' and resid 345 through 347 removed outlier: 3.897A pdb=" N THR 6 345 " --> pdb=" O PHE 6 409 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE 6 409 " --> pdb=" O THR 6 345 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AH5, first strand: chain 'A' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE A 26 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 72 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 73 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL A 38 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.572A pdb=" N GLU C 4 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.637A pdb=" N GLU B 4 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE B 26 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 72 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 73 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL B 38 " --> pdb=" O HIS B 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE C 26 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG C 72 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 73 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 38 through 39 removed outlier: 4.558A pdb=" N VAL C 38 " --> pdb=" O HIS C 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AI5, first strand: chain 'D' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE D 26 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG D 72 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 73 " --> pdb=" O ILE D 87 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL D 38 " --> pdb=" O HIS D 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.659A pdb=" N GLU F 4 " --> pdb=" O PHE D 65 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.590A pdb=" N GLU E 4 " --> pdb=" O PHE F 65 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE E 26 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 72 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 73 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL E 38 " --> pdb=" O HIS E 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE F 26 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 72 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 73 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL F 38 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.573A pdb=" N GLU G 4 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE G 26 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG G 72 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY G 73 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL G 38 " --> pdb=" O HIS G 48 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.538A pdb=" N GLU I 4 " --> pdb=" O PHE G 65 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.738A pdb=" N GLU H 4 " --> pdb=" O PHE I 65 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE H 26 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG H 72 " --> pdb=" O TYR H 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY H 73 " --> pdb=" O ILE H 87 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL H 38 " --> pdb=" O HIS H 48 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE I 26 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG I 72 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY I 73 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL I 38 " --> pdb=" O HIS I 48 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLU J 4 " --> pdb=" O PHE K 65 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE J 26 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG J 72 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY J 73 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 38 through 39 removed outlier: 4.556A pdb=" N VAL J 38 " --> pdb=" O HIS J 48 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 64 through 66 removed outlier: 3.641A pdb=" N GLU L 4 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.738A pdb=" N GLU K 4 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'K' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE K 26 " --> pdb=" O VAL K 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG K 72 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY K 73 " --> pdb=" O ILE K 87 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'K' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL K 38 " --> pdb=" O HIS K 48 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE L 26 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG L 72 " --> pdb=" O TYR L 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY L 73 " --> pdb=" O ILE L 87 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'L' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL L 38 " --> pdb=" O HIS L 48 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'M' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE M 26 " --> pdb=" O VAL M 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG M 72 " --> pdb=" O TYR M 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 73 " --> pdb=" O ILE M 87 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'M' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL M 38 " --> pdb=" O HIS M 48 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'M' and resid 64 through 66 removed outlier: 3.670A pdb=" N GLU O 4 " --> pdb=" O PHE M 65 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 24 through 28 removed outlier: 3.626A pdb=" N PHE N 26 " --> pdb=" O VAL N 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG N 72 " --> pdb=" O TYR N 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY N 73 " --> pdb=" O ILE N 87 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'N' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL N 38 " --> pdb=" O HIS N 48 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'O' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE O 26 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG O 72 " --> pdb=" O TYR O 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY O 73 " --> pdb=" O ILE O 87 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'O' and resid 38 through 39 removed outlier: 4.556A pdb=" N VAL O 38 " --> pdb=" O HIS O 48 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 3 through 5 removed outlier: 3.601A pdb=" N GLU P 4 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE P 26 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG P 72 " --> pdb=" O TYR P 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY P 73 " --> pdb=" O ILE P 87 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'P' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL P 38 " --> pdb=" O HIS P 48 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'P' and resid 64 through 66 removed outlier: 3.547A pdb=" N GLU R 4 " --> pdb=" O PHE P 65 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Q' and resid 3 through 5 removed outlier: 3.703A pdb=" N GLU Q 4 " --> pdb=" O PHE R 65 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Q' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE Q 26 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG Q 72 " --> pdb=" O TYR Q 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY Q 73 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Q' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL Q 38 " --> pdb=" O HIS Q 48 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'R' and resid 24 through 28 removed outlier: 3.627A pdb=" N PHE R 26 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG R 72 " --> pdb=" O TYR R 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY R 73 " --> pdb=" O ILE R 87 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'R' and resid 38 through 39 removed outlier: 4.557A pdb=" N VAL R 38 " --> pdb=" O HIS R 48 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1296 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: 12.82 Time building geometry restraints manager: 13.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11015 1.34 - 1.45: 6155 1.45 - 1.57: 17774 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 35052 Sorted by residual: bond pdb=" C ASP P 88 " pdb=" N PRO P 89 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.02e+00 bond pdb=" C ASP A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.94e+00 bond pdb=" C ASP J 88 " pdb=" N PRO J 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 bond pdb=" C ASP C 88 " pdb=" N PRO C 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.89e+00 bond pdb=" C ASP F 88 " pdb=" N PRO F 89 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.88e+00 ... (remaining 35047 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.09: 733 106.09 - 113.20: 18299 113.20 - 120.30: 12965 120.30 - 127.40: 15487 127.40 - 134.51: 306 Bond angle restraints: 47790 Sorted by residual: angle pdb=" C TYR 3 325 " pdb=" N ASP 3 326 " pdb=" CA ASP 3 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.49e+01 angle pdb=" C TYR 6 325 " pdb=" N ASP 6 326 " pdb=" CA ASP 6 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.48e+01 angle pdb=" C TYR 1 325 " pdb=" N ASP 1 326 " pdb=" CA ASP 1 326 " ideal model delta sigma weight residual 122.46 130.78 -8.32 1.41e+00 5.03e-01 3.48e+01 angle pdb=" C TYR 4 325 " pdb=" N ASP 4 326 " pdb=" CA ASP 4 326 " ideal model delta sigma weight residual 122.46 130.75 -8.29 1.41e+00 5.03e-01 3.46e+01 angle pdb=" C TYR 5 325 " pdb=" N ASP 5 326 " pdb=" CA ASP 5 326 " ideal model delta sigma weight residual 122.46 130.75 -8.29 1.41e+00 5.03e-01 3.46e+01 ... (remaining 47785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 18864 14.90 - 29.79: 1056 29.79 - 44.69: 246 44.69 - 59.58: 6 59.58 - 74.48: 24 Dihedral angle restraints: 20196 sinusoidal: 7458 harmonic: 12738 Sorted by residual: dihedral pdb=" CA PHE 4 76 " pdb=" C PHE 4 76 " pdb=" N TYR 4 77 " pdb=" CA TYR 4 77 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE 5 76 " pdb=" C PHE 5 76 " pdb=" N TYR 5 77 " pdb=" CA TYR 5 77 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE 1 76 " pdb=" C PHE 1 76 " pdb=" N TYR 1 77 " pdb=" CA TYR 1 77 " ideal model delta harmonic sigma weight residual 180.00 153.01 26.99 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3414 0.046 - 0.091: 1415 0.091 - 0.137: 409 0.137 - 0.182: 72 0.182 - 0.228: 54 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ASP 5 326 " pdb=" N ASP 5 326 " pdb=" C ASP 5 326 " pdb=" CB ASP 5 326 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ASP 2 326 " pdb=" N ASP 2 326 " pdb=" C ASP 2 326 " pdb=" CB ASP 2 326 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASP 4 326 " pdb=" N ASP 4 326 " pdb=" C ASP 4 326 " pdb=" CB ASP 4 326 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 5361 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 5 411 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO 5 412 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 5 412 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 5 412 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 411 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO 3 412 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO 3 412 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO 3 412 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 2 411 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO 2 412 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " -0.034 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 10973 2.83 - 3.35: 27640 3.35 - 3.87: 55008 3.87 - 4.38: 61203 4.38 - 4.90: 107921 Nonbonded interactions: 262745 Sorted by model distance: nonbonded pdb=" OG SER 6 30 " pdb=" O GLN 6 33 " model vdw 2.316 2.440 nonbonded pdb=" OG SER 2 30 " pdb=" O GLN 2 33 " model vdw 2.316 2.440 nonbonded pdb=" OG SER 5 30 " pdb=" O GLN 5 33 " model vdw 2.316 2.440 nonbonded pdb=" OG SER 1 30 " pdb=" O GLN 1 33 " model vdw 2.317 2.440 nonbonded pdb=" OG SER 4 30 " pdb=" O GLN 4 33 " model vdw 2.317 2.440 ... (remaining 262740 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 '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.100 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: 0.020 Extract box with map and model: 11.500 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 86.300 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 0.067 35052 Z= 0.372 Angle : 0.978 12.064 47790 Z= 0.540 Chirality : 0.056 0.228 5364 Planarity : 0.008 0.062 6240 Dihedral : 10.423 74.481 12108 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.17 % Allowed : 3.53 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.09), residues: 4440 helix: -5.17 (0.07), residues: 168 sheet: -3.01 (0.15), residues: 852 loop : -3.43 (0.08), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP O 25 HIS 0.005 0.002 HIS 4 285 PHE 0.035 0.003 PHE 1 76 TYR 0.017 0.003 TYR 3 239 ARG 0.011 0.001 ARG 3 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 378 time to evaluate : 3.994 Fit side-chains REVERT: A 74 VAL cc_start: 0.7939 (m) cc_final: 0.7485 (p) REVERT: A 85 TYR cc_start: 0.6583 (m-80) cc_final: 0.6333 (m-80) REVERT: B 1 MET cc_start: 0.2909 (mtp) cc_final: 0.2640 (mtt) REVERT: B 97 VAL cc_start: 0.4316 (t) cc_final: 0.3944 (p) REVERT: C 38 VAL cc_start: 0.7896 (t) cc_final: 0.7694 (m) REVERT: D 74 VAL cc_start: 0.7937 (m) cc_final: 0.7510 (p) REVERT: E 1 MET cc_start: 0.3277 (mtp) cc_final: 0.2791 (mtt) REVERT: E 97 VAL cc_start: 0.3936 (t) cc_final: 0.3514 (p) REVERT: F 14 SER cc_start: 0.7518 (p) cc_final: 0.7305 (t) REVERT: F 86 ASP cc_start: 0.7784 (t0) cc_final: 0.7518 (t70) REVERT: G 74 VAL cc_start: 0.8109 (m) cc_final: 0.7737 (p) REVERT: H 1 MET cc_start: 0.2622 (mtp) cc_final: 0.2231 (mtt) REVERT: H 97 VAL cc_start: 0.4006 (t) cc_final: 0.3719 (p) REVERT: I 55 ASP cc_start: 0.7628 (m-30) cc_final: 0.7407 (m-30) REVERT: I 91 ASN cc_start: 0.6760 (t0) cc_final: 0.6481 (t0) REVERT: J 66 ASP cc_start: 0.6470 (t0) cc_final: 0.6214 (t0) REVERT: J 74 VAL cc_start: 0.8108 (m) cc_final: 0.7675 (p) REVERT: K 5 LEU cc_start: 0.8189 (tt) cc_final: 0.7823 (tp) REVERT: K 97 VAL cc_start: 0.4367 (t) cc_final: 0.4026 (p) REVERT: L 14 SER cc_start: 0.7824 (p) cc_final: 0.7571 (t) REVERT: L 86 ASP cc_start: 0.7720 (t0) cc_final: 0.7467 (t0) REVERT: M 74 VAL cc_start: 0.8105 (m) cc_final: 0.7710 (p) REVERT: N 1 MET cc_start: 0.3379 (mtp) cc_final: 0.2866 (mtt) REVERT: N 97 VAL cc_start: 0.3650 (t) cc_final: 0.3358 (p) REVERT: O 87 ILE cc_start: 0.8757 (mp) cc_final: 0.8441 (mt) REVERT: O 91 ASN cc_start: 0.6178 (t0) cc_final: 0.5785 (t0) REVERT: P 74 VAL cc_start: 0.8056 (m) cc_final: 0.7666 (p) REVERT: Q 1 MET cc_start: 0.2714 (mtp) cc_final: 0.2255 (mtt) REVERT: Q 97 VAL cc_start: 0.4117 (t) cc_final: 0.3839 (p) REVERT: R 86 ASP cc_start: 0.7758 (t0) cc_final: 0.6766 (p0) REVERT: R 91 ASN cc_start: 0.6574 (t0) cc_final: 0.6279 (t0) outliers start: 6 outliers final: 0 residues processed: 384 average time/residue: 0.3721 time to fit residues: 248.7537 Evaluate side-chains 174 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 8.9990 chunk 336 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 403 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN ** 1 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 285 HIS 1 417 GLN 2 33 GLN 2 246 GLN 2 285 HIS ** 2 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 33 GLN 3 246 GLN 3 285 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 33 GLN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 285 HIS ** 4 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 33 GLN 5 246 GLN 5 285 HIS 5 417 GLN 6 33 GLN 6 246 GLN 6 285 HIS ** 6 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 36 GLN F 6 HIS F 19 ASN F 91 ASN I 6 HIS J 29 GLN L 6 HIS L 19 ASN L 36 GLN O 6 HIS O 19 ASN R 6 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35052 Z= 0.313 Angle : 0.714 9.256 47790 Z= 0.368 Chirality : 0.047 0.152 5364 Planarity : 0.006 0.048 6240 Dihedral : 6.153 24.647 4842 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 1.26 % Allowed : 8.46 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.10), residues: 4440 helix: -4.98 (0.09), residues: 150 sheet: -2.51 (0.15), residues: 924 loop : -3.12 (0.09), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 5 320 HIS 0.006 0.002 HIS 5 285 PHE 0.025 0.002 PHE 1 76 TYR 0.018 0.002 TYR G 39 ARG 0.006 0.001 ARG 3 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 3.734 Fit side-chains REVERT: A 85 TYR cc_start: 0.6725 (m-80) cc_final: 0.6401 (m-80) REVERT: B 1 MET cc_start: 0.2458 (mtp) cc_final: 0.2035 (mtm) REVERT: C 86 ASP cc_start: 0.7756 (t0) cc_final: 0.6909 (p0) REVERT: E 1 MET cc_start: 0.2913 (mtp) cc_final: 0.2229 (mtt) REVERT: F 86 ASP cc_start: 0.7544 (t0) cc_final: 0.7054 (p0) REVERT: F 91 ASN cc_start: 0.6641 (OUTLIER) cc_final: 0.5892 (t0) REVERT: H 1 MET cc_start: 0.2361 (mtp) cc_final: 0.1720 (mtt) REVERT: H 95 LEU cc_start: 0.6459 (mt) cc_final: 0.6181 (mp) REVERT: I 86 ASP cc_start: 0.7580 (t0) cc_final: 0.6909 (p0) REVERT: L 14 SER cc_start: 0.7752 (p) cc_final: 0.7374 (t) REVERT: L 86 ASP cc_start: 0.7678 (t0) cc_final: 0.7256 (p0) REVERT: N 1 MET cc_start: 0.3366 (mtp) cc_final: 0.2729 (mtt) REVERT: O 86 ASP cc_start: 0.7538 (t70) cc_final: 0.6723 (p0) REVERT: Q 1 MET cc_start: 0.2524 (mtp) cc_final: 0.1851 (mtt) REVERT: R 86 ASP cc_start: 0.7595 (t0) cc_final: 0.7365 (p0) REVERT: R 91 ASN cc_start: 0.6911 (t0) cc_final: 0.6525 (t0) outliers start: 45 outliers final: 21 residues processed: 232 average time/residue: 0.3646 time to fit residues: 153.2401 Evaluate side-chains 184 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain F residue 16 ASN Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain R residue 16 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 274 optimal weight: 0.2980 chunk 111 optimal weight: 10.0000 chunk 403 optimal weight: 30.0000 chunk 436 optimal weight: 6.9990 chunk 359 optimal weight: 30.0000 chunk 400 optimal weight: 40.0000 chunk 137 optimal weight: 0.8980 chunk 324 optimal weight: 20.0000 overall best weight: 5.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 246 GLN 2 417 GLN 3 38 GLN 3 417 GLN 4 246 GLN 4 417 GLN 6 38 GLN 6 417 GLN C 19 ASN E 6 HIS H 6 HIS I 91 ASN J 29 GLN N 6 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35052 Z= 0.275 Angle : 0.663 8.119 47790 Z= 0.344 Chirality : 0.046 0.281 5364 Planarity : 0.005 0.045 6240 Dihedral : 5.813 25.836 4842 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.30 % Allowed : 9.50 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.11), residues: 4440 helix: -5.50 (0.13), residues: 42 sheet: -2.01 (0.16), residues: 966 loop : -2.88 (0.09), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 5 320 HIS 0.005 0.001 HIS E 48 PHE 0.017 0.002 PHE 3 76 TYR 0.014 0.002 TYR H 28 ARG 0.004 0.001 ARG 5 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 167 time to evaluate : 3.867 Fit side-chains REVERT: 3 373 MET cc_start: 0.8584 (ptm) cc_final: 0.8188 (tmm) REVERT: 3 442 ARG cc_start: 0.6002 (OUTLIER) cc_final: 0.5689 (ppp80) REVERT: A 69 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6134 (pp) REVERT: B 1 MET cc_start: 0.2456 (mtp) cc_final: 0.2201 (mtm) REVERT: B 69 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6991 (pp) REVERT: C 86 ASP cc_start: 0.7674 (t0) cc_final: 0.7014 (p0) REVERT: E 1 MET cc_start: 0.3217 (mtp) cc_final: 0.2426 (mtt) REVERT: E 69 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6877 (pp) REVERT: E 95 LEU cc_start: 0.6630 (mp) cc_final: 0.5824 (tp) REVERT: F 86 ASP cc_start: 0.7573 (t0) cc_final: 0.7145 (p0) REVERT: F 91 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6267 (t0) REVERT: G 69 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6732 (pp) REVERT: H 69 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6655 (pp) REVERT: H 95 LEU cc_start: 0.6391 (mt) cc_final: 0.6110 (mp) REVERT: I 86 ASP cc_start: 0.7557 (t0) cc_final: 0.6942 (p0) REVERT: I 91 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6124 (t0) REVERT: J 75 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6812 (tp) REVERT: L 86 ASP cc_start: 0.7529 (t0) cc_final: 0.7295 (p0) REVERT: N 1 MET cc_start: 0.3187 (mtp) cc_final: 0.2451 (mtt) REVERT: O 86 ASP cc_start: 0.7529 (t70) cc_final: 0.6968 (p0) REVERT: P 69 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6697 (pp) REVERT: Q 95 LEU cc_start: 0.6476 (mt) cc_final: 0.6162 (mp) REVERT: R 86 ASP cc_start: 0.7679 (t0) cc_final: 0.7455 (p0) REVERT: R 91 ASN cc_start: 0.6930 (t0) cc_final: 0.6538 (t0) outliers start: 82 outliers final: 37 residues processed: 236 average time/residue: 0.3677 time to fit residues: 155.9223 Evaluate side-chains 198 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 91 ASN Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 2.9990 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 405 optimal weight: 30.0000 chunk 429 optimal weight: 0.0870 chunk 211 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN I 91 ASN P 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35052 Z= 0.281 Angle : 0.654 7.574 47790 Z= 0.339 Chirality : 0.045 0.197 5364 Planarity : 0.005 0.045 6240 Dihedral : 5.741 26.296 4842 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 3.14 % Allowed : 10.45 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.11), residues: 4440 helix: -5.50 (0.13), residues: 42 sheet: -1.90 (0.16), residues: 996 loop : -2.75 (0.09), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 5 320 HIS 0.005 0.001 HIS E 48 PHE 0.018 0.002 PHE F 65 TYR 0.013 0.002 TYR Q 28 ARG 0.004 0.001 ARG 1 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 170 time to evaluate : 4.160 Fit side-chains REVERT: 2 422 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: 2 442 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5948 (ppp80) REVERT: 5 422 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: 5 442 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5947 (ppp80) REVERT: A 69 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.6041 (pp) REVERT: A 75 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6990 (tp) REVERT: B 69 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7033 (pp) REVERT: B 95 LEU cc_start: 0.6911 (mm) cc_final: 0.6496 (mp) REVERT: C 86 ASP cc_start: 0.7675 (t0) cc_final: 0.7238 (p0) REVERT: E 1 MET cc_start: 0.3091 (mtp) cc_final: 0.2328 (mtt) REVERT: E 69 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6925 (pp) REVERT: E 95 LEU cc_start: 0.6751 (mp) cc_final: 0.6138 (tp) REVERT: F 70 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6548 (tp30) REVERT: H 69 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6664 (pp) REVERT: H 95 LEU cc_start: 0.6241 (mt) cc_final: 0.5962 (tp) REVERT: I 86 ASP cc_start: 0.7544 (t70) cc_final: 0.7018 (p0) REVERT: J 75 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6794 (tp) REVERT: K 95 LEU cc_start: 0.6379 (mm) cc_final: 0.5883 (tp) REVERT: N 1 MET cc_start: 0.3013 (mtp) cc_final: 0.2200 (mtt) REVERT: N 69 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7034 (pp) REVERT: O 86 ASP cc_start: 0.7542 (t70) cc_final: 0.7041 (p0) REVERT: P 69 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6546 (pp) REVERT: Q 95 LEU cc_start: 0.6087 (mt) cc_final: 0.5803 (mp) outliers start: 112 outliers final: 71 residues processed: 270 average time/residue: 0.3878 time to fit residues: 184.3901 Evaluate side-chains 233 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 150 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 82 LEU Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 16 ASN Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 18 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 21 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 16 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 319 optimal weight: 0.0060 chunk 177 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 0.7980 chunk 385 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN C 19 ASN F 91 ASN Q 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35052 Z= 0.182 Angle : 0.571 7.011 47790 Z= 0.296 Chirality : 0.043 0.158 5364 Planarity : 0.004 0.039 6240 Dihedral : 5.199 22.616 4842 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.83 % Allowed : 12.07 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.11), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.76 (0.16), residues: 966 loop : -2.62 (0.10), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 6 320 HIS 0.003 0.001 HIS B 48 PHE 0.010 0.001 PHE 5 76 TYR 0.011 0.001 TYR Q 39 ARG 0.003 0.000 ARG 6 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 170 time to evaluate : 4.218 Fit side-chains REVERT: 1 422 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: 2 442 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5823 (ppp80) REVERT: 3 442 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5840 (ppp80) REVERT: 4 422 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: 5 442 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5812 (ppp80) REVERT: A 75 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6825 (tp) REVERT: B 69 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.7061 (pp) REVERT: B 95 LEU cc_start: 0.6825 (mm) cc_final: 0.6042 (tp) REVERT: C 86 ASP cc_start: 0.7647 (t70) cc_final: 0.7223 (p0) REVERT: E 1 MET cc_start: 0.3354 (mtp) cc_final: 0.2497 (mtt) REVERT: E 69 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7074 (pp) REVERT: E 95 LEU cc_start: 0.6660 (mp) cc_final: 0.5989 (tt) REVERT: F 91 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6291 (t0) REVERT: H 69 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6615 (pp) REVERT: H 95 LEU cc_start: 0.6088 (mt) cc_final: 0.5775 (tt) REVERT: I 86 ASP cc_start: 0.7643 (t70) cc_final: 0.7169 (p0) REVERT: J 75 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6788 (tp) REVERT: K 95 LEU cc_start: 0.6141 (mm) cc_final: 0.5718 (tp) REVERT: M 21 ASP cc_start: 0.6283 (p0) cc_final: 0.6028 (p0) REVERT: M 75 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6923 (tp) REVERT: N 1 MET cc_start: 0.3259 (mtp) cc_final: 0.2387 (mtt) REVERT: N 69 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7220 (pp) REVERT: O 86 ASP cc_start: 0.7600 (t70) cc_final: 0.7002 (p0) REVERT: P 69 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6401 (pp) REVERT: Q 95 LEU cc_start: 0.6181 (mt) cc_final: 0.5840 (tp) outliers start: 101 outliers final: 58 residues processed: 261 average time/residue: 0.3936 time to fit residues: 181.4959 Evaluate side-chains 228 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 156 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 1 residue 442 ARG Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 4 residue 442 ARG Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 91 ASN Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain R residue 16 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 20.0000 chunk 386 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 251 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 429 optimal weight: 0.0050 chunk 356 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 0.0370 chunk 225 optimal weight: 20.0000 overall best weight: 2.8274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35052 Z= 0.173 Angle : 0.558 6.650 47790 Z= 0.291 Chirality : 0.043 0.154 5364 Planarity : 0.004 0.036 6240 Dihedral : 5.029 24.532 4842 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 3.00 % Allowed : 12.63 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.61 (0.16), residues: 1038 loop : -2.52 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 3 320 HIS 0.003 0.001 HIS H 48 PHE 0.012 0.001 PHE 6 335 TYR 0.009 0.001 TYR B 39 ARG 0.002 0.000 ARG 3 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 157 time to evaluate : 4.250 Fit side-chains REVERT: 1 422 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: 2 422 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: 2 442 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5848 (ppp80) REVERT: 3 442 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5818 (ppp80) REVERT: 4 422 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: 5 422 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7221 (m-30) REVERT: 5 442 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5890 (ppp80) REVERT: A 75 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6847 (tp) REVERT: B 69 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7061 (pp) REVERT: B 95 LEU cc_start: 0.6740 (mm) cc_final: 0.5977 (tp) REVERT: C 86 ASP cc_start: 0.7645 (t70) cc_final: 0.7222 (p0) REVERT: E 1 MET cc_start: 0.3394 (mtp) cc_final: 0.2524 (mtt) REVERT: E 95 LEU cc_start: 0.6628 (mp) cc_final: 0.5914 (tt) REVERT: G 75 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6165 (tp) REVERT: H 69 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6675 (pp) REVERT: H 95 LEU cc_start: 0.6102 (mt) cc_final: 0.5761 (tt) REVERT: I 86 ASP cc_start: 0.7704 (t70) cc_final: 0.7126 (p0) REVERT: J 75 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6787 (tp) REVERT: K 95 LEU cc_start: 0.6112 (mm) cc_final: 0.5699 (mp) REVERT: M 21 ASP cc_start: 0.6234 (p0) cc_final: 0.5982 (p0) REVERT: M 75 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6892 (tp) REVERT: N 1 MET cc_start: 0.3177 (mtp) cc_final: 0.2419 (mtt) REVERT: N 69 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7151 (pp) REVERT: O 86 ASP cc_start: 0.7617 (t70) cc_final: 0.6987 (p0) REVERT: P 75 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6167 (tp) REVERT: Q 60 PHE cc_start: 0.7567 (m-80) cc_final: 0.7198 (m-10) REVERT: Q 95 LEU cc_start: 0.6079 (mt) cc_final: 0.5668 (tt) outliers start: 107 outliers final: 67 residues processed: 251 average time/residue: 0.3928 time to fit residues: 173.7793 Evaluate side-chains 236 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 108 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 244 optimal weight: 0.2980 chunk 313 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 361 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN L 91 ASN P 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35052 Z= 0.201 Angle : 0.571 7.119 47790 Z= 0.297 Chirality : 0.043 0.157 5364 Planarity : 0.004 0.037 6240 Dihedral : 5.061 23.330 4842 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 3.56 % Allowed : 12.69 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.60 (0.15), residues: 1068 loop : -2.44 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 320 HIS 0.004 0.001 HIS H 48 PHE 0.012 0.001 PHE 5 76 TYR 0.010 0.001 TYR K 39 ARG 0.003 0.000 ARG 6 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 153 time to evaluate : 4.603 Fit side-chains REVERT: 1 422 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: 2 59 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7794 (pp30) REVERT: 2 422 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: 2 442 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5903 (ppp80) REVERT: 3 442 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5866 (ppp80) REVERT: 4 422 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: 5 59 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7779 (pp30) REVERT: 5 422 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: 5 442 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5901 (ppp80) REVERT: A 75 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6885 (tp) REVERT: B 69 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7088 (pp) REVERT: C 70 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6493 (tp30) REVERT: C 86 ASP cc_start: 0.7516 (t70) cc_final: 0.7119 (p0) REVERT: E 1 MET cc_start: 0.3315 (mtp) cc_final: 0.2466 (mtt) REVERT: E 95 LEU cc_start: 0.6607 (mp) cc_final: 0.5972 (tt) REVERT: G 75 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6223 (tp) REVERT: H 69 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6659 (pp) REVERT: H 95 LEU cc_start: 0.6136 (mt) cc_final: 0.5807 (tt) REVERT: I 86 ASP cc_start: 0.7689 (t70) cc_final: 0.7122 (p0) REVERT: J 75 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6763 (tp) REVERT: K 95 LEU cc_start: 0.6248 (mm) cc_final: 0.5833 (mp) REVERT: L 70 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6518 (tp30) REVERT: M 21 ASP cc_start: 0.6226 (p0) cc_final: 0.5970 (p0) REVERT: N 1 MET cc_start: 0.3201 (mtp) cc_final: 0.2403 (mtt) REVERT: O 86 ASP cc_start: 0.7617 (t70) cc_final: 0.6998 (p0) REVERT: P 75 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6129 (tp) REVERT: Q 60 PHE cc_start: 0.7586 (m-80) cc_final: 0.7242 (m-10) REVERT: Q 95 LEU cc_start: 0.6100 (mt) cc_final: 0.5701 (tt) outliers start: 127 outliers final: 86 residues processed: 267 average time/residue: 0.3755 time to fit residues: 176.5698 Evaluate side-chains 250 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 149 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 431 VAL Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 108 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 255 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 272 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 38 GLN K 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35052 Z= 0.272 Angle : 0.625 7.442 47790 Z= 0.325 Chirality : 0.045 0.215 5364 Planarity : 0.004 0.037 6240 Dihedral : 5.414 25.858 4842 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.81 % Allowed : 12.83 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.58 (0.16), residues: 1044 loop : -2.45 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 3 320 HIS 0.005 0.001 HIS B 48 PHE 0.014 0.001 PHE 2 76 TYR 0.012 0.002 TYR B 39 ARG 0.004 0.000 ARG 6 427 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 151 time to evaluate : 3.471 Fit side-chains REVERT: 1 177 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7912 (tp) REVERT: 1 422 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: 2 59 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: 2 422 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: 2 442 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.6042 (ppp80) REVERT: 3 442 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5914 (ppp80) REVERT: 4 177 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7921 (tp) REVERT: 4 422 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: 5 59 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7790 (pp30) REVERT: 5 422 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: 5 442 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.6115 (ppp80) REVERT: 6 59 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: A 75 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6888 (tp) REVERT: B 69 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7133 (pp) REVERT: C 70 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6557 (tp30) REVERT: C 86 ASP cc_start: 0.7424 (t70) cc_final: 0.7147 (p0) REVERT: E 1 MET cc_start: 0.3211 (mtp) cc_final: 0.2573 (mtp) REVERT: E 95 LEU cc_start: 0.6494 (mp) cc_final: 0.5882 (tt) REVERT: G 75 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6163 (tp) REVERT: H 69 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6708 (pp) REVERT: H 95 LEU cc_start: 0.6420 (mt) cc_final: 0.5986 (tt) REVERT: I 86 ASP cc_start: 0.7646 (t70) cc_final: 0.7206 (p0) REVERT: J 75 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6796 (tp) REVERT: K 95 LEU cc_start: 0.6368 (mm) cc_final: 0.5958 (mp) REVERT: L 70 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6608 (tp30) REVERT: M 21 ASP cc_start: 0.6201 (p0) cc_final: 0.5913 (p0) REVERT: N 1 MET cc_start: 0.3247 (mtp) cc_final: 0.2720 (mtp) REVERT: O 86 ASP cc_start: 0.7572 (t70) cc_final: 0.6965 (p0) REVERT: P 75 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6145 (tp) REVERT: Q 95 LEU cc_start: 0.6198 (mt) cc_final: 0.5752 (tt) outliers start: 136 outliers final: 95 residues processed: 276 average time/residue: 0.3837 time to fit residues: 186.1848 Evaluate side-chains 258 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 145 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 289 VAL Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 431 VAL Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 108 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 289 VAL Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 431 VAL Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 59 GLN Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain F residue 16 ASN Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 91 ASN Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 6.9990 chunk 409 optimal weight: 0.0170 chunk 374 optimal weight: 6.9990 chunk 398 optimal weight: 30.0000 chunk 240 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 360 optimal weight: 20.0000 chunk 377 optimal weight: 7.9990 chunk 397 optimal weight: 8.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35052 Z= 0.265 Angle : 0.626 7.459 47790 Z= 0.326 Chirality : 0.045 0.183 5364 Planarity : 0.004 0.037 6240 Dihedral : 5.423 25.609 4842 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.59 % Allowed : 13.42 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.59 (0.16), residues: 1062 loop : -2.43 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 1 320 HIS 0.005 0.001 HIS H 48 PHE 0.012 0.001 PHE 3 76 TYR 0.011 0.001 TYR B 39 ARG 0.004 0.000 ARG 1 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 149 time to evaluate : 3.872 Fit side-chains REVERT: 1 177 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7902 (tp) REVERT: 1 422 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: 2 59 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7792 (pp30) REVERT: 2 422 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: 2 442 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.6043 (ppp80) REVERT: 3 442 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5873 (ppp80) REVERT: 4 177 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7905 (tp) REVERT: 4 422 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: 5 59 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7786 (pp30) REVERT: 5 422 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: 5 442 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.6048 (ppp80) REVERT: 6 59 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: A 75 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.6886 (tp) REVERT: B 69 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7139 (pp) REVERT: C 66 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7073 (m-30) REVERT: C 70 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6558 (tp30) REVERT: C 86 ASP cc_start: 0.7428 (t70) cc_final: 0.7163 (p0) REVERT: E 1 MET cc_start: 0.3081 (mtp) cc_final: 0.2458 (mtp) REVERT: E 95 LEU cc_start: 0.6473 (mp) cc_final: 0.5844 (tt) REVERT: G 75 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6106 (tp) REVERT: H 69 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6738 (pp) REVERT: H 95 LEU cc_start: 0.6462 (mt) cc_final: 0.6031 (tt) REVERT: I 86 ASP cc_start: 0.7700 (t70) cc_final: 0.7314 (p0) REVERT: J 75 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6790 (tp) REVERT: K 4 GLU cc_start: 0.7523 (tp30) cc_final: 0.7096 (tm-30) REVERT: K 59 LYS cc_start: 0.7479 (mtpt) cc_final: 0.7178 (ttpt) REVERT: K 95 LEU cc_start: 0.6458 (mm) cc_final: 0.6033 (mp) REVERT: L 70 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6592 (tp30) REVERT: M 21 ASP cc_start: 0.6196 (p0) cc_final: 0.5905 (p0) REVERT: N 1 MET cc_start: 0.3222 (mtp) cc_final: 0.2674 (mtp) REVERT: O 86 ASP cc_start: 0.7558 (t70) cc_final: 0.6957 (p0) REVERT: P 75 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6354 (tp) REVERT: Q 95 LEU cc_start: 0.6301 (mt) cc_final: 0.5848 (tt) outliers start: 128 outliers final: 96 residues processed: 269 average time/residue: 0.3982 time to fit residues: 188.3730 Evaluate side-chains 262 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 147 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 59 GLN Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 371 LEU Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 2 residue 59 GLN Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 431 VAL Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 108 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 59 GLN Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 177 LEU Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 371 LEU Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 108 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 431 VAL Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 59 GLN Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 431 VAL Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain F residue 16 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 90 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 442 optimal weight: 0.7980 chunk 407 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS E 36 GLN N 36 GLN Q 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35052 Z= 0.167 Angle : 0.563 7.266 47790 Z= 0.293 Chirality : 0.043 0.171 5364 Planarity : 0.004 0.035 6240 Dihedral : 5.019 23.082 4842 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.97 % Allowed : 14.20 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.56 (0.15), residues: 1098 loop : -2.32 (0.10), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 1 320 HIS 0.003 0.001 HIS H 48 PHE 0.010 0.001 PHE 2 76 TYR 0.011 0.001 TYR Q 39 ARG 0.002 0.000 ARG 4 427 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 160 time to evaluate : 3.857 Fit side-chains REVERT: 1 422 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: 2 422 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: 2 442 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5870 (ppp80) REVERT: 3 442 ARG cc_start: 0.6042 (OUTLIER) cc_final: 0.5773 (ppp80) REVERT: 4 422 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: 5 59 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7810 (pp30) REVERT: 5 422 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: 5 442 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5920 (ppp80) REVERT: A 75 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6806 (tp) REVERT: B 69 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7192 (pp) REVERT: C 59 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7469 (ttpt) REVERT: C 70 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6541 (tp30) REVERT: C 86 ASP cc_start: 0.7432 (t70) cc_final: 0.7163 (p0) REVERT: E 1 MET cc_start: 0.2989 (mtp) cc_final: 0.2578 (mtp) REVERT: E 95 LEU cc_start: 0.6445 (mp) cc_final: 0.5833 (tt) REVERT: G 21 ASP cc_start: 0.5944 (p0) cc_final: 0.5603 (p0) REVERT: G 75 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.5992 (tp) REVERT: H 69 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6763 (pp) REVERT: H 95 LEU cc_start: 0.6516 (mt) cc_final: 0.6110 (tt) REVERT: I 86 ASP cc_start: 0.7707 (t70) cc_final: 0.7322 (p0) REVERT: J 75 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6719 (tp) REVERT: K 4 GLU cc_start: 0.7384 (tp30) cc_final: 0.7026 (tm-30) REVERT: K 59 LYS cc_start: 0.7443 (mtpt) cc_final: 0.7210 (ttpt) REVERT: K 95 LEU cc_start: 0.6402 (mm) cc_final: 0.5948 (mp) REVERT: L 66 ASP cc_start: 0.7785 (m-30) cc_final: 0.7192 (t0) REVERT: L 70 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6577 (tp30) REVERT: M 21 ASP cc_start: 0.6188 (p0) cc_final: 0.5934 (p0) REVERT: M 75 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6783 (tp) REVERT: N 1 MET cc_start: 0.3219 (mtp) cc_final: 0.2613 (mtp) REVERT: O 86 ASP cc_start: 0.7561 (t70) cc_final: 0.6949 (p0) REVERT: P 21 ASP cc_start: 0.5923 (p0) cc_final: 0.5709 (p0) REVERT: P 75 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6006 (tp) REVERT: Q 95 LEU cc_start: 0.6383 (mt) cc_final: 0.5859 (tt) outliers start: 106 outliers final: 82 residues processed: 256 average time/residue: 0.3916 time to fit residues: 175.3638 Evaluate side-chains 253 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 155 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 76 PHE Chi-restraints excluded: chain 1 residue 83 LEU Chi-restraints excluded: chain 1 residue 108 LEU Chi-restraints excluded: chain 1 residue 124 GLU Chi-restraints excluded: chain 1 residue 129 THR Chi-restraints excluded: chain 1 residue 130 ILE Chi-restraints excluded: chain 1 residue 320 TRP Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 431 VAL Chi-restraints excluded: chain 2 residue 76 PHE Chi-restraints excluded: chain 2 residue 83 LEU Chi-restraints excluded: chain 2 residue 108 LEU Chi-restraints excluded: chain 2 residue 129 THR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 320 TRP Chi-restraints excluded: chain 2 residue 422 ASP Chi-restraints excluded: chain 2 residue 442 ARG Chi-restraints excluded: chain 3 residue 76 PHE Chi-restraints excluded: chain 3 residue 82 LEU Chi-restraints excluded: chain 3 residue 83 LEU Chi-restraints excluded: chain 3 residue 129 THR Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 320 TRP Chi-restraints excluded: chain 3 residue 431 VAL Chi-restraints excluded: chain 3 residue 442 ARG Chi-restraints excluded: chain 4 residue 76 PHE Chi-restraints excluded: chain 4 residue 83 LEU Chi-restraints excluded: chain 4 residue 108 LEU Chi-restraints excluded: chain 4 residue 124 GLU Chi-restraints excluded: chain 4 residue 129 THR Chi-restraints excluded: chain 4 residue 130 ILE Chi-restraints excluded: chain 4 residue 320 TRP Chi-restraints excluded: chain 4 residue 422 ASP Chi-restraints excluded: chain 4 residue 431 VAL Chi-restraints excluded: chain 5 residue 59 GLN Chi-restraints excluded: chain 5 residue 76 PHE Chi-restraints excluded: chain 5 residue 83 LEU Chi-restraints excluded: chain 5 residue 108 LEU Chi-restraints excluded: chain 5 residue 129 THR Chi-restraints excluded: chain 5 residue 130 ILE Chi-restraints excluded: chain 5 residue 320 TRP Chi-restraints excluded: chain 5 residue 422 ASP Chi-restraints excluded: chain 5 residue 442 ARG Chi-restraints excluded: chain 6 residue 76 PHE Chi-restraints excluded: chain 6 residue 82 LEU Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 130 ILE Chi-restraints excluded: chain 6 residue 320 TRP Chi-restraints excluded: chain 6 residue 442 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 90 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain L residue 16 ASN Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 37 SER Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 52 VAL Chi-restraints excluded: chain O residue 66 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain Q residue 21 ASP Chi-restraints excluded: chain R residue 16 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 90 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.0670 chunk 375 optimal weight: 0.4980 chunk 107 optimal weight: 20.0000 chunk 324 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 352 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 overall best weight: 3.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054618 restraints weight = 182011.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055454 restraints weight = 117970.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055991 restraints weight = 85084.094| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35052 Z= 0.196 Angle : 0.573 7.114 47790 Z= 0.298 Chirality : 0.043 0.171 5364 Planarity : 0.004 0.035 6240 Dihedral : 5.039 23.763 4842 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 3.11 % Allowed : 14.20 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.50 (0.16), residues: 1068 loop : -2.32 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 1 320 HIS 0.004 0.001 HIS H 48 PHE 0.012 0.001 PHE 5 76 TYR 0.011 0.001 TYR N 39 ARG 0.003 0.000 ARG 6 427 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5218.74 seconds wall clock time: 96 minutes 34.43 seconds (5794.43 seconds total)