Starting phenix.real_space_refine on Sat Dec 16 06:50:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/12_2023/7eeq_31080.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/12_2023/7eeq_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_31080/12_2023/7eeq_31080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/12_2023/7eeq_31080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/12_2023/7eeq_31080.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eeq_31080/12_2023/7eeq_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.95, per 1000 atoms: 0.49 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: 12.10 Conformation dependent library (CDL) restraints added in 7.1 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: 3.73 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: 13.42 Time building geometry restraints manager: 13.22 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 12.060 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 86.860 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.410 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.080 ------------------------------------------------------------------------------- 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 : 3.863 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 384 average time/residue: 0.3957 time to fit residues: 263.8814 Evaluate side-chains 163 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8993 ------------------------------------------------------------------------------- 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: 30.0000 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: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 1 285 HIS 1 417 GLN 2 33 GLN 2 246 GLN 2 285 HIS 2 417 GLN 3 33 GLN 3 246 GLN 3 285 HIS 3 417 GLN 4 33 GLN 4 246 GLN 4 285 HIS 4 417 GLN 5 33 GLN 5 246 GLN 5 285 HIS 5 417 GLN 6 33 GLN 6 246 GLN 6 285 HIS 6 417 GLN A 29 GLN C 36 GLN D 29 GLN F 19 ASN F 91 ASN J 29 GLN L 19 ASN L 36 GLN M 29 GLN O 19 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35052 Z= 0.265 Angle : 0.673 8.744 47790 Z= 0.349 Chirality : 0.046 0.148 5364 Planarity : 0.006 0.045 6240 Dihedral : 5.994 23.594 4842 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 1.40 % Allowed : 7.93 % Favored : 90.67 % 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: -4.29 (0.10), residues: 4440 helix: -5.12 (0.08), residues: 168 sheet: -2.43 (0.15), residues: 924 loop : -3.11 (0.09), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 5 320 HIS 0.005 0.001 HIS K 6 PHE 0.020 0.002 PHE 1 76 TYR 0.016 0.002 TYR Q 39 ARG 0.004 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 235 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 3.567 Fit side-chains outliers start: 50 outliers final: 26 residues processed: 228 average time/residue: 0.3703 time to fit residues: 153.7799 Evaluate side-chains 183 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 3.984 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3443 time to fit residues: 21.8808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 335 optimal weight: 20.0000 chunk 274 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 403 optimal weight: 40.0000 chunk 436 optimal weight: 20.0000 chunk 359 optimal weight: 9.9990 chunk 400 optimal weight: 30.0000 chunk 137 optimal weight: 0.5980 chunk 324 optimal weight: 20.0000 overall best weight: 8.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN C 6 HIS C 19 ASN D 29 GLN F 6 HIS H 6 HIS I 6 HIS J 29 GLN L 6 HIS M 29 GLN N 6 HIS O 6 HIS Q 6 HIS R 6 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 35052 Z= 0.371 Angle : 0.749 9.303 47790 Z= 0.388 Chirality : 0.048 0.287 5364 Planarity : 0.006 0.049 6240 Dihedral : 6.283 28.872 4842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 1.71 % Allowed : 10.08 % 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: -3.85 (0.11), residues: 4440 helix: -5.51 (0.13), residues: 42 sheet: -2.10 (0.15), residues: 1026 loop : -2.91 (0.09), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP 5 320 HIS 0.007 0.002 HIS B 6 PHE 0.021 0.002 PHE 3 76 TYR 0.019 0.002 TYR H 28 ARG 0.005 0.001 ARG 6 224 *********************** 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 226 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 165 time to evaluate : 3.989 Fit side-chains outliers start: 61 outliers final: 28 residues processed: 216 average time/residue: 0.3866 time to fit residues: 148.4549 Evaluate side-chains 177 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3491 time to fit residues: 22.5816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.0980 chunk 303 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 405 optimal weight: 20.0000 chunk 429 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 384 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 38 GLN C 19 ASN D 36 GLN M 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35052 Z= 0.206 Angle : 0.615 7.776 47790 Z= 0.318 Chirality : 0.044 0.192 5364 Planarity : 0.004 0.041 6240 Dihedral : 5.614 24.584 4842 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.60 % Allowed : 11.74 % Favored : 86.67 % 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: -3.63 (0.11), residues: 4440 helix: -5.50 (0.13), residues: 42 sheet: -1.88 (0.16), residues: 1002 loop : -2.77 (0.09), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 4 320 HIS 0.004 0.001 HIS H 48 PHE 0.013 0.001 PHE I 65 TYR 0.012 0.001 TYR Q 39 ARG 0.003 0.000 ARG 6 427 *********************** 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 220 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 3.588 Fit side-chains outliers start: 57 outliers final: 26 residues processed: 216 average time/residue: 0.3833 time to fit residues: 148.3772 Evaluate side-chains 175 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 3.769 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3015 time to fit residues: 19.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 319 optimal weight: 30.0000 chunk 177 optimal weight: 9.9990 chunk 366 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 385 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35052 Z= 0.222 Angle : 0.604 6.797 47790 Z= 0.314 Chirality : 0.044 0.160 5364 Planarity : 0.004 0.040 6240 Dihedral : 5.424 24.348 4842 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 1.99 % Allowed : 12.10 % Favored : 85.91 % 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: -3.50 (0.11), residues: 4440 helix: -5.50 (0.13), residues: 42 sheet: -1.79 (0.16), residues: 1002 loop : -2.68 (0.10), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 1 320 HIS 0.004 0.001 HIS H 48 PHE 0.013 0.001 PHE 6 335 TYR 0.012 0.001 TYR N 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 232 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 161 time to evaluate : 4.090 Fit side-chains outliers start: 71 outliers final: 28 residues processed: 221 average time/residue: 0.3997 time to fit residues: 157.8408 Evaluate side-chains 170 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.887 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3575 time to fit residues: 22.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 84 optimal weight: 9.9990 chunk 251 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 429 optimal weight: 20.0000 chunk 356 optimal weight: 20.0000 chunk 198 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35052 Z= 0.302 Angle : 0.660 8.365 47790 Z= 0.343 Chirality : 0.046 0.277 5364 Planarity : 0.005 0.040 6240 Dihedral : 5.706 26.558 4842 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 1.20 % Allowed : 13.73 % Favored : 85.07 % 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: -1.78 (0.15), residues: 1092 loop : -2.63 (0.10), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 1 320 HIS 0.006 0.001 HIS H 48 PHE 0.020 0.002 PHE 6 76 TYR 0.012 0.002 TYR N 39 ARG 0.003 0.001 ARG 6 224 *********************** 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 195 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 3.604 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 190 average time/residue: 0.3879 time to fit residues: 135.0084 Evaluate side-chains 175 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 4.210 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3154 time to fit residues: 21.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 244 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 243 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 260 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 38 GLN A 36 GLN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN J 36 GLN L 19 ASN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35052 Z= 0.295 Angle : 0.660 7.893 47790 Z= 0.343 Chirality : 0.046 0.208 5364 Planarity : 0.005 0.041 6240 Dihedral : 5.723 26.414 4842 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 1.18 % Allowed : 14.31 % Favored : 84.51 % 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: -3.38 (0.11), residues: 4440 helix: -5.16 (0.17), residues: 48 sheet: -1.68 (0.15), residues: 1056 loop : -2.60 (0.10), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 1 320 HIS 0.006 0.001 HIS H 48 PHE 0.017 0.002 PHE 3 76 TYR 0.014 0.002 TYR N 39 ARG 0.004 0.001 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 199 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 4.147 Fit side-chains outliers start: 42 outliers final: 22 residues processed: 194 average time/residue: 0.4048 time to fit residues: 140.1087 Evaluate side-chains 169 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4137 time to fit residues: 20.4665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 255 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 272 optimal weight: 0.3980 chunk 291 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35052 Z= 0.239 Angle : 0.621 8.962 47790 Z= 0.323 Chirality : 0.045 0.216 5364 Planarity : 0.004 0.042 6240 Dihedral : 5.499 25.160 4842 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.73 % Allowed : 15.18 % Favored : 84.09 % 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: -3.29 (0.12), residues: 4440 helix: -5.49 (0.13), residues: 42 sheet: -1.64 (0.15), residues: 1080 loop : -2.53 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 3 320 HIS 0.005 0.001 HIS H 48 PHE 0.014 0.001 PHE 6 76 TYR 0.012 0.001 TYR N 39 ARG 0.003 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 177 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 4.139 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 174 average time/residue: 0.3914 time to fit residues: 124.9503 Evaluate side-chains 161 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3401 time to fit residues: 13.6380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 240 optimal weight: 0.0040 chunk 173 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 360 optimal weight: 0.8980 chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 6.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS C 91 ASN K 6 HIS L 91 ASN N 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35052 Z= 0.191 Angle : 0.584 8.043 47790 Z= 0.303 Chirality : 0.044 0.186 5364 Planarity : 0.004 0.036 6240 Dihedral : 5.188 23.549 4842 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.36 % Allowed : 15.66 % Favored : 83.98 % 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: -3.18 (0.12), residues: 4440 helix: -5.48 (0.13), residues: 42 sheet: -1.49 (0.16), residues: 1050 loop : -2.47 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 4 320 HIS 0.004 0.001 HIS H 48 PHE 0.011 0.001 PHE 3 335 TYR 0.011 0.001 TYR N 39 ARG 0.002 0.000 ARG 4 427 *********************** 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 165 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 3.970 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.4153 time to fit residues: 122.8118 Evaluate side-chains 155 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 3.706 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3305 time to fit residues: 9.1791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 293 optimal weight: 0.0470 chunk 442 optimal weight: 20.0000 chunk 407 optimal weight: 3.9990 chunk 352 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 overall best weight: 6.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 ASN K 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35052 Z= 0.311 Angle : 0.671 8.659 47790 Z= 0.350 Chirality : 0.046 0.233 5364 Planarity : 0.005 0.042 6240 Dihedral : 5.690 26.974 4842 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.20 % Allowed : 15.94 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.12), residues: 4440 helix: -5.48 (0.13), residues: 42 sheet: -1.69 (0.15), residues: 1092 loop : -2.50 (0.10), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP 4 320 HIS 0.007 0.001 HIS H 48 PHE 0.018 0.002 PHE 3 76 TYR 0.014 0.002 TYR H 39 ARG 0.004 0.001 ARG 3 427 ********************** 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 155 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 3.809 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 155 average time/residue: 0.3923 time to fit residues: 110.4235 Evaluate side-chains 151 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 3.820 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3165 time to fit residues: 7.0549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 6.9990 chunk 375 optimal weight: 40.0000 chunk 107 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 352 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 362 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.060854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054091 restraints weight = 181536.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054880 restraints weight = 117142.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055460 restraints weight = 84541.880| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35052 Z= 0.237 Angle : 0.623 8.573 47790 Z= 0.324 Chirality : 0.045 0.173 5364 Planarity : 0.004 0.039 6240 Dihedral : 5.479 25.450 4842 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.08 % Allowed : 16.44 % Favored : 83.47 % 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: -3.21 (0.12), residues: 4440 helix: -5.48 (0.13), residues: 42 sheet: -1.60 (0.15), residues: 1080 loop : -2.47 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 4 320 HIS 0.005 0.001 HIS H 48 PHE 0.013 0.001 PHE 6 76 TYR 0.013 0.001 TYR H 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: 4799.46 seconds wall clock time: 90 minutes 4.61 seconds (5404.61 seconds total)