Starting phenix.real_space_refine on Fri Mar 22 03:37:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/03_2024/8pho_17669.pdb" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 96 5.16 5 C 20400 2.51 5 N 4992 2.21 5 O 6684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32172 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE A 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE A 407 " pdbres="HOH A 501 " Not linked: pdbres="HOH A 501 " pdbres="HOH A 502 " Not linked: pdbres="HOH A 502 " pdbres="HOH A 503 " Not linked: pdbres="HOH A 503 " pdbres="HOH A 504 " Not linked: pdbres="HOH A 504 " pdbres="HOH A 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "B" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE B 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE B 407 " pdbres="HOH B 501 " Not linked: pdbres="HOH B 501 " pdbres="HOH B 502 " Not linked: pdbres="HOH B 502 " pdbres="HOH B 503 " Not linked: pdbres="HOH B 503 " pdbres="HOH B 504 " Not linked: pdbres="HOH B 504 " pdbres="HOH B 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "C" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE C 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE C 407 " pdbres="HOH C 501 " Not linked: pdbres="HOH C 501 " pdbres="HOH C 502 " Not linked: pdbres="HOH C 502 " pdbres="HOH C 503 " Not linked: pdbres="HOH C 503 " pdbres="HOH C 504 " Not linked: pdbres="HOH C 504 " pdbres="HOH C 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "D" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE D 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE D 407 " pdbres="HOH D 501 " Not linked: pdbres="HOH D 501 " pdbres="HOH D 502 " Not linked: pdbres="HOH D 502 " pdbres="HOH D 503 " Not linked: pdbres="HOH D 503 " pdbres="HOH D 504 " Not linked: pdbres="HOH D 504 " pdbres="HOH D 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "E" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE E 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE E 407 " pdbres="HOH E 501 " Not linked: pdbres="HOH E 501 " pdbres="HOH E 502 " Not linked: pdbres="HOH E 502 " pdbres="HOH E 503 " Not linked: pdbres="HOH E 503 " pdbres="HOH E 504 " Not linked: pdbres="HOH E 504 " pdbres="HOH E 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "F" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE F 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE F 407 " pdbres="HOH F 501 " Not linked: pdbres="HOH F 501 " pdbres="HOH F 502 " Not linked: pdbres="HOH F 502 " pdbres="HOH F 503 " Not linked: pdbres="HOH F 503 " pdbres="HOH F 504 " Not linked: pdbres="HOH F 504 " pdbres="HOH F 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "G" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE G 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE G 407 " pdbres="HOH G 501 " Not linked: pdbres="HOH G 501 " pdbres="HOH G 502 " Not linked: pdbres="HOH G 502 " pdbres="HOH G 503 " Not linked: pdbres="HOH G 503 " pdbres="HOH G 504 " Not linked: pdbres="HOH G 504 " pdbres="HOH G 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "H" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE H 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE H 407 " pdbres="HOH H 501 " Not linked: pdbres="HOH H 501 " pdbres="HOH H 502 " Not linked: pdbres="HOH H 502 " pdbres="HOH H 503 " Not linked: pdbres="HOH H 503 " pdbres="HOH H 504 " Not linked: pdbres="HOH H 504 " pdbres="HOH H 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "I" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE I 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE I 407 " pdbres="HOH I 501 " Not linked: pdbres="HOH I 501 " pdbres="HOH I 502 " Not linked: pdbres="HOH I 502 " pdbres="HOH I 503 " Not linked: pdbres="HOH I 503 " pdbres="HOH I 504 " Not linked: pdbres="HOH I 504 " pdbres="HOH I 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "J" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE J 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE J 407 " pdbres="HOH J 501 " Not linked: pdbres="HOH J 501 " pdbres="HOH J 502 " Not linked: pdbres="HOH J 502 " pdbres="HOH J 503 " Not linked: pdbres="HOH J 503 " pdbres="HOH J 504 " Not linked: pdbres="HOH J 504 " pdbres="HOH J 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "K" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE K 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE K 407 " pdbres="HOH K 501 " Not linked: pdbres="HOH K 501 " pdbres="HOH K 502 " Not linked: pdbres="HOH K 502 " pdbres="HOH K 503 " Not linked: pdbres="HOH K 503 " pdbres="HOH K 504 " Not linked: pdbres="HOH K 504 " pdbres="HOH K 505 " ... (remaining 55 not shown) Chain breaks: 2 Chain: "L" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2681 Inner-chain residues flagged as termini: ['pdbres="PHE L 407 "'] Classifications: {'peptide': 317, 'water': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 311, None: 60} Not linked: pdbres="PHE L 407 " pdbres="HOH L 501 " Not linked: pdbres="HOH L 501 " pdbres="HOH L 502 " Not linked: pdbres="HOH L 502 " pdbres="HOH L 503 " Not linked: pdbres="HOH L 503 " pdbres="HOH L 504 " Not linked: pdbres="HOH L 504 " pdbres="HOH L 505 " ... (remaining 55 not shown) Chain breaks: 2 Time building chain proxies: 17.07, per 1000 atoms: 0.53 Number of scatterers: 32172 At special positions: 0 Unit cell: (170.888, 170.888, 120.872, 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 96 16.00 O 6684 8.00 N 4992 7.00 C 20400 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: 13.81 Conformation dependent library (CDL) restraints added in 6.1 seconds 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 60 sheets defined 53.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU A 93 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 389 Processing helix chain 'A' and resid 393 through 404 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL B 32 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU B 93 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 349 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 389 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU C 93 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 393 through 404 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL D 32 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D 33 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU D 93 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU E 93 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 303 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 389 Processing helix chain 'E' and resid 393 through 404 Processing helix chain 'F' and resid 14 through 22 Processing helix chain 'F' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL F 32 " --> pdb=" O TYR F 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU F 93 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR F 177 " --> pdb=" O PHE F 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 303 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR F 349 " --> pdb=" O ASN F 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS F 350 " --> pdb=" O LEU F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 389 Processing helix chain 'F' and resid 393 through 404 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU G 93 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 178 " --> pdb=" O GLU G 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 303 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 389 Processing helix chain 'G' and resid 393 through 404 Processing helix chain 'H' and resid 14 through 22 Processing helix chain 'H' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL H 32 " --> pdb=" O TYR H 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA H 33 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 37 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU H 93 " --> pdb=" O ILE H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 178 " --> pdb=" O GLU H 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 303 Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS H 347 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR H 349 " --> pdb=" O ASN H 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS H 350 " --> pdb=" O LEU H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 389 Processing helix chain 'H' and resid 393 through 404 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL I 32 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU I 93 " --> pdb=" O ILE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR I 177 " --> pdb=" O PHE I 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 178 " --> pdb=" O GLU I 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 303 Processing helix chain 'I' and resid 305 through 310 Processing helix chain 'I' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 349 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 389 Processing helix chain 'I' and resid 393 through 404 Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL J 32 " --> pdb=" O TYR J 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU J 93 " --> pdb=" O ILE J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR J 177 " --> pdb=" O PHE J 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 178 " --> pdb=" O GLU J 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 303 Processing helix chain 'J' and resid 305 through 310 Processing helix chain 'J' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR J 349 " --> pdb=" O ASN J 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS J 350 " --> pdb=" O LEU J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL K 32 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 77 removed outlier: 3.819A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU K 93 " --> pdb=" O ILE K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 178 " --> pdb=" O GLU K 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 303 Processing helix chain 'K' and resid 305 through 310 Processing helix chain 'K' and resid 327 through 353 removed outlier: 4.402A pdb=" N LYS K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR K 349 " --> pdb=" O ASN K 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 389 Processing helix chain 'K' and resid 393 through 404 Processing helix chain 'L' and resid 14 through 22 Processing helix chain 'L' and resid 22 through 37 removed outlier: 4.708A pdb=" N VAL L 32 " --> pdb=" O TYR L 28 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA L 33 " --> pdb=" O ILE L 29 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 77 removed outlier: 3.820A pdb=" N ASN L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.529A pdb=" N GLU L 93 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 110 No H-bonds generated for 'chain 'L' and resid 108 through 110' Processing helix chain 'L' and resid 163 through 184 removed outlier: 4.385A pdb=" N TYR L 177 " --> pdb=" O PHE L 173 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 303 Processing helix chain 'L' and resid 305 through 310 Processing helix chain 'L' and resid 327 through 353 removed outlier: 4.401A pdb=" N LYS L 347 " --> pdb=" O SER L 343 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR L 349 " --> pdb=" O ASN L 345 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS L 350 " --> pdb=" O LEU L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 389 Processing helix chain 'L' and resid 393 through 404 Processing sheet with id= 1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id= 2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id= 4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id= 5, first strand: chain 'A' and resid 188 through 193 Processing sheet with id= 6, first strand: chain 'B' and resid 41 through 45 Processing sheet with id= 7, first strand: chain 'B' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR B 80 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 112 through 113 Processing sheet with id= 9, first strand: chain 'B' and resid 151 through 152 Processing sheet with id= 10, first strand: chain 'B' and resid 188 through 193 Processing sheet with id= 11, first strand: chain 'C' and resid 41 through 45 Processing sheet with id= 12, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR C 80 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 112 through 113 Processing sheet with id= 14, first strand: chain 'C' and resid 151 through 152 Processing sheet with id= 15, first strand: chain 'C' and resid 188 through 193 Processing sheet with id= 16, first strand: chain 'D' and resid 41 through 45 Processing sheet with id= 17, first strand: chain 'D' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR D 80 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 112 through 113 Processing sheet with id= 19, first strand: chain 'D' and resid 151 through 152 Processing sheet with id= 20, first strand: chain 'D' and resid 188 through 193 Processing sheet with id= 21, first strand: chain 'E' and resid 41 through 45 Processing sheet with id= 22, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR E 80 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'E' and resid 112 through 113 Processing sheet with id= 24, first strand: chain 'E' and resid 151 through 152 Processing sheet with id= 25, first strand: chain 'E' and resid 188 through 193 Processing sheet with id= 26, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 27, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR F 80 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'F' and resid 112 through 113 Processing sheet with id= 29, first strand: chain 'F' and resid 151 through 152 Processing sheet with id= 30, first strand: chain 'F' and resid 188 through 193 Processing sheet with id= 31, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 32, first strand: chain 'G' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR G 80 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 112 through 113 Processing sheet with id= 34, first strand: chain 'G' and resid 151 through 152 Processing sheet with id= 35, first strand: chain 'G' and resid 188 through 193 Processing sheet with id= 36, first strand: chain 'H' and resid 41 through 45 Processing sheet with id= 37, first strand: chain 'H' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR H 80 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 112 through 113 Processing sheet with id= 39, first strand: chain 'H' and resid 151 through 152 Processing sheet with id= 40, first strand: chain 'H' and resid 188 through 193 Processing sheet with id= 41, first strand: chain 'I' and resid 41 through 45 Processing sheet with id= 42, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR I 80 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'I' and resid 112 through 113 Processing sheet with id= 44, first strand: chain 'I' and resid 151 through 152 Processing sheet with id= 45, first strand: chain 'I' and resid 188 through 193 Processing sheet with id= 46, first strand: chain 'J' and resid 41 through 45 Processing sheet with id= 47, first strand: chain 'J' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR J 80 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 112 through 113 Processing sheet with id= 49, first strand: chain 'J' and resid 151 through 152 Processing sheet with id= 50, first strand: chain 'J' and resid 188 through 193 Processing sheet with id= 51, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 52, first strand: chain 'K' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR K 80 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 112 through 113 Processing sheet with id= 54, first strand: chain 'K' and resid 151 through 152 Processing sheet with id= 55, first strand: chain 'K' and resid 188 through 193 Processing sheet with id= 56, first strand: chain 'L' and resid 41 through 45 Processing sheet with id= 57, first strand: chain 'L' and resid 103 through 107 removed outlier: 4.588A pdb=" N TYR L 80 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'L' and resid 112 through 113 Processing sheet with id= 59, first strand: chain 'L' and resid 151 through 152 Processing sheet with id= 60, first strand: chain 'L' and resid 188 through 193 1740 hydrogen bonds defined for protein. 5040 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: 11.23 Time building geometry restraints manager: 14.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9912 1.34 - 1.46: 7388 1.46 - 1.58: 14596 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 32040 Sorted by residual: bond pdb=" CB ASN E 394 " pdb=" CG ASN E 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN B 394 " pdb=" CG ASN B 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN H 394 " pdb=" CG ASN H 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN K 394 " pdb=" CG ASN K 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN J 394 " pdb=" CG ASN J 394 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.77e+00 ... (remaining 32035 not shown) Histogram of bond angle deviations from ideal: 100.69 - 106.89: 372 106.89 - 113.09: 16384 113.09 - 119.29: 9716 119.29 - 125.48: 16536 125.48 - 131.68: 120 Bond angle restraints: 43128 Sorted by residual: angle pdb=" CB ARG J 326 " pdb=" CG ARG J 326 " pdb=" CD ARG J 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG A 326 " pdb=" CG ARG A 326 " pdb=" CD ARG A 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG D 326 " pdb=" CG ARG D 326 " pdb=" CD ARG D 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG G 326 " pdb=" CG ARG G 326 " pdb=" CD ARG G 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 angle pdb=" CB ARG F 326 " pdb=" CG ARG F 326 " pdb=" CD ARG F 326 " ideal model delta sigma weight residual 111.30 116.66 -5.36 2.30e+00 1.89e-01 5.43e+00 ... (remaining 43123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 17616 16.52 - 33.03: 1296 33.03 - 49.55: 288 49.55 - 66.07: 96 66.07 - 82.58: 60 Dihedral angle restraints: 19356 sinusoidal: 8004 harmonic: 11352 Sorted by residual: dihedral pdb=" CB GLU F 266 " pdb=" CG GLU F 266 " pdb=" CD GLU F 266 " pdb=" OE1 GLU F 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU L 266 " pdb=" CG GLU L 266 " pdb=" CD GLU L 266 " pdb=" OE1 GLU L 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 dihedral pdb=" CB GLU I 266 " pdb=" CG GLU I 266 " pdb=" CD GLU I 266 " pdb=" OE1 GLU I 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 ... (remaining 19353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4208 0.085 - 0.171: 484 0.171 - 0.256: 12 0.256 - 0.341: 48 0.341 - 0.427: 12 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CG LEU I 115 " pdb=" CB LEU I 115 " pdb=" CD1 LEU I 115 " pdb=" CD2 LEU I 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU L 115 " pdb=" CB LEU L 115 " pdb=" CD1 LEU L 115 " pdb=" CD2 LEU L 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU F 115 " pdb=" CB LEU F 115 " pdb=" CD1 LEU F 115 " pdb=" CD2 LEU F 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 4761 not shown) Planarity restraints: 5448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN L 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN L 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN L 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN I 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN I 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN I 150 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 150 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" CG ASN C 150 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 150 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 5445 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 396 2.68 - 3.24: 30172 3.24 - 3.79: 50584 3.79 - 4.35: 72748 4.35 - 4.90: 113644 Nonbonded interactions: 267544 Sorted by model distance: nonbonded pdb=" O HOH G 502 " pdb=" O HOH G 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH D 502 " pdb=" O HOH D 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH J 502 " pdb=" O HOH J 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 533 " model vdw 2.128 2.440 nonbonded pdb=" O HOH I 502 " pdb=" O HOH I 533 " model vdw 2.128 2.440 ... (remaining 267539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.710 Check model and map are aligned: 0.510 Set scattering table: 0.270 Process input model: 85.950 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.200 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.044 32040 Z= 0.290 Angle : 0.767 5.989 43128 Z= 0.406 Chirality : 0.062 0.427 4764 Planarity : 0.010 0.072 5448 Dihedral : 13.642 82.583 12060 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: -0.02 (0.13), residues: 3732 helix: 0.55 (0.11), residues: 2004 sheet: -0.38 (0.21), residues: 624 loop : -0.58 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.024 0.007 HIS E 48 PHE 0.034 0.008 PHE I 358 TYR 0.036 0.008 TYR D 192 ARG 0.023 0.005 ARG I 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 696 time to evaluate : 4.001 Fit side-chains REVERT: A 181 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: A 382 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7647 (mmmt) REVERT: A 403 LYS cc_start: 0.6967 (ptmt) cc_final: 0.6558 (ptmt) REVERT: B 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: C 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7383 (p-80) REVERT: C 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7307 (mp0) REVERT: C 363 MET cc_start: 0.7463 (mtp) cc_final: 0.7080 (mmt) REVERT: C 382 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7606 (mmmt) REVERT: D 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6818 (mmt180) REVERT: D 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: D 403 LYS cc_start: 0.6963 (ptmt) cc_final: 0.6555 (ptmt) REVERT: E 382 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7690 (mptt) REVERT: F 121 HIS cc_start: 0.7593 (p-80) cc_final: 0.7384 (p-80) REVERT: F 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: F 363 MET cc_start: 0.7467 (mtp) cc_final: 0.7082 (mmt) REVERT: F 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7608 (mmmt) REVERT: G 181 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7868 (tm-30) REVERT: G 326 ARG cc_start: 0.7114 (mmt90) cc_final: 0.6819 (mmt180) REVERT: G 382 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7646 (mmmt) REVERT: G 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: H 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: I 121 HIS cc_start: 0.7592 (p-80) cc_final: 0.7382 (p-80) REVERT: I 185 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7308 (mp0) REVERT: I 363 MET cc_start: 0.7466 (mtp) cc_final: 0.7082 (mmt) REVERT: I 382 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7609 (mmmt) REVERT: J 181 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7868 (tm-30) REVERT: J 326 ARG cc_start: 0.7115 (mmt90) cc_final: 0.6820 (mmt180) REVERT: J 382 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7644 (mmmt) REVERT: J 403 LYS cc_start: 0.6964 (ptmt) cc_final: 0.6556 (ptmt) REVERT: K 382 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7689 (mptt) REVERT: L 121 HIS cc_start: 0.7591 (p-80) cc_final: 0.7382 (p-80) REVERT: L 185 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7306 (mp0) REVERT: L 363 MET cc_start: 0.7465 (mtp) cc_final: 0.7080 (mmt) REVERT: L 382 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7610 (mmmt) outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 1.9566 time to fit residues: 1536.2214 Evaluate side-chains 492 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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: 0.0040 chunk 336 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 179 optimal weight: 0.0050 chunk 348 optimal weight: 0.0570 chunk 134 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 403 optimal weight: 50.0000 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 121 HIS A 314 GLN A 368 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 314 GLN B 337 GLN B 388 GLN C 76 HIS C 314 GLN C 388 GLN C 393 ASN D 94 GLN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN E 320 ASN F 76 HIS F 314 GLN F 393 ASN G 94 GLN G 187 HIS G 314 GLN G 320 ASN G 368 GLN G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN H 314 GLN I 76 HIS I 314 GLN I 393 ASN J 76 HIS J 94 GLN J 121 HIS J 314 GLN J 368 GLN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** K 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN L 312 ASN L 314 GLN ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.168 32040 Z= 0.423 Angle : 1.276 28.224 43128 Z= 0.667 Chirality : 0.067 0.790 4764 Planarity : 0.018 0.449 5448 Dihedral : 6.004 132.736 4200 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.59 % Rotamer: Outliers : 3.22 % Allowed : 9.94 % Favored : 86.84 % Cbeta Deviations : 0.11 % 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: -1.44 (0.12), residues: 3732 helix: -0.68 (0.11), residues: 2004 sheet: -0.93 (0.20), residues: 624 loop : -1.09 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.055 0.005 HIS L 76 PHE 0.177 0.009 PHE H 119 TYR 0.276 0.008 TYR J 383 ARG 0.110 0.004 ARG I 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 584 time to evaluate : 3.854 Fit side-chains REVERT: A 55 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 121 HIS cc_start: 0.7510 (p90) cc_final: 0.7256 (p90) REVERT: A 326 ARG cc_start: 0.7184 (mmt90) cc_final: 0.6934 (mmt180) REVERT: A 372 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7756 (mtm180) REVERT: A 382 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7677 (mmmt) REVERT: B 382 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7678 (mmmt) REVERT: C 55 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 57 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: C 357 LYS cc_start: 0.7852 (tppt) cc_final: 0.7530 (tttm) REVERT: C 382 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7598 (mmmt) REVERT: D 121 HIS cc_start: 0.7636 (p-80) cc_final: 0.7304 (p90) REVERT: D 326 ARG cc_start: 0.7192 (mmt90) cc_final: 0.6920 (mmt180) REVERT: E 120 ASP cc_start: 0.7354 (p0) cc_final: 0.6949 (p0) REVERT: E 121 HIS cc_start: 0.7691 (p-80) cc_final: 0.7004 (m-70) REVERT: E 382 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7725 (mmmt) REVERT: F 111 TYR cc_start: 0.8462 (m-10) cc_final: 0.8230 (m-10) REVERT: F 121 HIS cc_start: 0.7643 (p-80) cc_final: 0.7438 (p-80) REVERT: F 144 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.8043 (mtt-85) REVERT: F 185 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7276 (mp0) REVERT: F 393 ASN cc_start: 0.5818 (OUTLIER) cc_final: 0.5437 (p0) REVERT: G 110 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: G 326 ARG cc_start: 0.7202 (mmt90) cc_final: 0.6974 (mmt180) REVERT: G 372 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7523 (mtm180) REVERT: G 382 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7685 (mmmt) REVERT: H 181 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: H 375 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7870 (mmtm) REVERT: H 382 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7616 (mptt) REVERT: I 55 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7331 (mp) REVERT: I 185 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7128 (mp0) REVERT: I 357 LYS cc_start: 0.7917 (tppt) cc_final: 0.7569 (tmtt) REVERT: I 363 MET cc_start: 0.7454 (mtp) cc_final: 0.6996 (mmt) REVERT: I 391 SER cc_start: 0.6412 (OUTLIER) cc_final: 0.5800 (m) REVERT: J 57 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6250 (ttp-170) REVERT: J 111 TYR cc_start: 0.8486 (m-10) cc_final: 0.8282 (m-10) REVERT: J 119 PHE cc_start: 0.7534 (m-80) cc_final: 0.7113 (m-80) REVERT: J 313 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: J 326 ARG cc_start: 0.7162 (mmt90) cc_final: 0.6883 (mmt180) REVERT: K 326 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7145 (mmt180) REVERT: K 382 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7743 (mmmt) REVERT: K 401 LYS cc_start: 0.6551 (mmmm) cc_final: 0.6329 (mmmm) REVERT: K 403 LYS cc_start: 0.7101 (ptpt) cc_final: 0.6785 (ptpt) REVERT: L 55 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7392 (mp) REVERT: L 110 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: L 121 HIS cc_start: 0.7599 (p-80) cc_final: 0.7379 (p-80) outliers start: 112 outliers final: 13 residues processed: 635 average time/residue: 1.9568 time to fit residues: 1403.7183 Evaluate side-chains 489 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 462 time to evaluate : 4.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 375 LYS Chi-restraints excluded: chain F residue 393 ASN Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 375 LYS Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 391 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 313 GLU Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 403 optimal weight: 50.0000 chunk 436 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 chunk 400 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 324 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 337 GLN C 314 GLN C 320 ASN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 314 GLN F 320 ASN F 339 GLN F 388 GLN F 393 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 GLN G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN H 388 GLN I 188 ASN I 314 GLN I 388 GLN I 393 ASN J 94 GLN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 368 GLN J 388 GLN K 61 GLN K 121 HIS ** K 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 388 GLN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32040 Z= 0.148 Angle : 0.467 4.983 43128 Z= 0.267 Chirality : 0.040 0.139 4764 Planarity : 0.004 0.049 5448 Dihedral : 5.053 174.160 4200 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.84 % Allowed : 11.41 % Favored : 86.75 % 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: 0.56 (0.14), residues: 3732 helix: 1.32 (0.12), residues: 2016 sheet: -0.55 (0.21), residues: 624 loop : -0.71 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 121 PHE 0.016 0.001 PHE E 269 TYR 0.024 0.002 TYR L 177 ARG 0.005 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 513 time to evaluate : 3.880 Fit side-chains revert: symmetry clash REVERT: A 119 PHE cc_start: 0.7528 (m-80) cc_final: 0.7103 (m-80) REVERT: A 181 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: A 326 ARG cc_start: 0.7310 (mmt90) cc_final: 0.7012 (mmt180) REVERT: B 120 ASP cc_start: 0.7195 (p0) cc_final: 0.6929 (p0) REVERT: B 181 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: C 55 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7257 (mp) REVERT: C 181 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7620 (pp20) REVERT: C 357 LYS cc_start: 0.8020 (tppt) cc_final: 0.7527 (tttm) REVERT: D 119 PHE cc_start: 0.7624 (m-80) cc_final: 0.7179 (m-80) REVERT: D 181 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: D 290 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: D 326 ARG cc_start: 0.7296 (mmt90) cc_final: 0.6979 (mmt180) REVERT: D 382 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7656 (mmmt) REVERT: E 120 ASP cc_start: 0.7349 (p0) cc_final: 0.7002 (p0) REVERT: E 121 HIS cc_start: 0.7762 (p-80) cc_final: 0.7531 (p-80) REVERT: E 144 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8072 (mtt-85) REVERT: E 181 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: E 357 LYS cc_start: 0.7977 (tppt) cc_final: 0.7681 (tttp) REVERT: E 401 LYS cc_start: 0.6457 (mmmm) cc_final: 0.6187 (mmmm) REVERT: F 121 HIS cc_start: 0.7659 (p-80) cc_final: 0.7432 (p-80) REVERT: F 185 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7188 (mp0) REVERT: F 402 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.6021 (mp0) REVERT: G 326 ARG cc_start: 0.7346 (mmt90) cc_final: 0.7041 (mmt180) REVERT: G 372 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7687 (mtm180) REVERT: H 181 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: H 326 ARG cc_start: 0.7377 (mmt-90) cc_final: 0.7153 (mmt180) REVERT: I 55 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7338 (mp) REVERT: I 144 ARG cc_start: 0.8226 (mtt-85) cc_final: 0.7892 (mtt-85) REVERT: I 185 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7182 (mp0) REVERT: J 20 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: J 181 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: J 326 ARG cc_start: 0.7307 (mmt90) cc_final: 0.6943 (mmt180) REVERT: J 372 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7049 (mtt180) REVERT: J 399 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5795 (tpt) REVERT: K 120 ASP cc_start: 0.7426 (p0) cc_final: 0.7099 (p0) REVERT: K 403 LYS cc_start: 0.7320 (ptpt) cc_final: 0.6864 (ptpt) REVERT: L 121 HIS cc_start: 0.7648 (p-80) cc_final: 0.7398 (p-80) outliers start: 64 outliers final: 10 residues processed: 544 average time/residue: 2.0112 time to fit residues: 1232.5149 Evaluate side-chains 470 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 446 time to evaluate : 4.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 57 ARG 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: 9.9990 chunk 209 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 192 optimal weight: 0.0570 chunk 271 optimal weight: 8.9990 chunk 405 optimal weight: 50.0000 chunk 429 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN B 121 HIS B 314 GLN B 320 ASN C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 94 GLN D 121 HIS ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN F 314 GLN F 388 GLN F 393 ASN G 314 GLN G 388 GLN G 393 ASN H 121 HIS H 314 GLN I 314 GLN I 388 GLN I 393 ASN J 94 GLN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 121 HIS L 312 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32040 Z= 0.172 Angle : 0.483 4.520 43128 Z= 0.275 Chirality : 0.040 0.139 4764 Planarity : 0.003 0.045 5448 Dihedral : 5.133 177.715 4200 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.81 % Allowed : 12.36 % Favored : 85.83 % 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: 1.05 (0.14), residues: 3732 helix: 1.63 (0.12), residues: 2028 sheet: -0.18 (0.22), residues: 600 loop : -0.45 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 121 PHE 0.021 0.002 PHE E 269 TYR 0.024 0.002 TYR L 177 ARG 0.004 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 467 time to evaluate : 3.854 Fit side-chains REVERT: A 181 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 326 ARG cc_start: 0.7371 (mmt90) cc_final: 0.7043 (mmt180) REVERT: A 403 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6991 (mtmm) REVERT: B 120 ASP cc_start: 0.7076 (p0) cc_final: 0.6729 (p0) REVERT: B 181 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: B 403 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6964 (pttm) REVERT: C 55 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7158 (mp) REVERT: C 120 ASP cc_start: 0.7272 (p0) cc_final: 0.6986 (p0) REVERT: C 181 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7851 (pp20) REVERT: D 181 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: D 290 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: D 326 ARG cc_start: 0.7319 (mmt90) cc_final: 0.6940 (mmt180) REVERT: D 341 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8028 (mt-10) REVERT: D 357 LYS cc_start: 0.7991 (tppt) cc_final: 0.7650 (ttpp) REVERT: E 120 ASP cc_start: 0.7304 (p0) cc_final: 0.6940 (p0) REVERT: E 121 HIS cc_start: 0.7900 (p-80) cc_final: 0.7514 (p90) REVERT: E 181 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: E 357 LYS cc_start: 0.8055 (tppt) cc_final: 0.7660 (tttp) REVERT: F 64 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7628 (t0) REVERT: F 121 HIS cc_start: 0.7746 (p-80) cc_final: 0.7495 (p-80) REVERT: F 185 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7152 (mp0) REVERT: F 326 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6875 (mmt180) REVERT: F 402 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: G 326 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6985 (mmt180) REVERT: H 181 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: H 326 ARG cc_start: 0.7491 (mmt-90) cc_final: 0.7116 (mmt180) REVERT: H 357 LYS cc_start: 0.7982 (tppt) cc_final: 0.7598 (tttm) REVERT: I 185 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7201 (mp0) REVERT: I 290 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: J 20 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: J 119 PHE cc_start: 0.7561 (m-80) cc_final: 0.7049 (m-80) REVERT: J 181 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: J 326 ARG cc_start: 0.7305 (mmt90) cc_final: 0.6917 (mmt180) REVERT: J 372 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7100 (mtt180) REVERT: K 120 ASP cc_start: 0.7342 (p0) cc_final: 0.7002 (p0) REVERT: K 144 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.8046 (mtt-85) REVERT: K 357 LYS cc_start: 0.8029 (tppt) cc_final: 0.7636 (tttm) REVERT: L 64 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7611 (t0) REVERT: L 121 HIS cc_start: 0.7667 (p-80) cc_final: 0.7405 (p-80) REVERT: L 403 LYS cc_start: 0.7298 (ttpt) cc_final: 0.6998 (mtmm) outliers start: 63 outliers final: 15 residues processed: 499 average time/residue: 1.9805 time to fit residues: 1117.0772 Evaluate side-chains 462 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 431 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 403 LYS Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 290 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 366 optimal weight: 50.0000 chunk 296 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 219 optimal weight: 50.0000 chunk 385 optimal weight: 8.9990 chunk 108 optimal weight: 50.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 320 ASN C 121 HIS C 314 GLN C 320 ASN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 HIS E 314 GLN E 388 GLN F 314 GLN F 320 ASN F 393 ASN G 187 HIS G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN H 388 GLN I 314 GLN I 320 ASN I 393 ASN J 121 HIS J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 GLN ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 388 GLN L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 32040 Z= 0.375 Angle : 0.665 5.671 43128 Z= 0.370 Chirality : 0.047 0.171 4764 Planarity : 0.005 0.063 5448 Dihedral : 5.789 174.443 4200 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.64 % Allowed : 11.18 % Favored : 86.18 % 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: 0.36 (0.13), residues: 3732 helix: 1.09 (0.12), residues: 2004 sheet: -0.39 (0.22), residues: 624 loop : -0.81 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 48 PHE 0.030 0.003 PHE I 269 TYR 0.030 0.003 TYR L 177 ARG 0.009 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 464 time to evaluate : 4.115 Fit side-chains REVERT: A 181 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: A 313 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: A 341 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 120 ASP cc_start: 0.7079 (p0) cc_final: 0.6723 (p0) REVERT: B 357 LYS cc_start: 0.8059 (tppt) cc_final: 0.7626 (tttm) REVERT: C 64 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 120 ASP cc_start: 0.7311 (p0) cc_final: 0.6996 (p0) REVERT: C 144 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7893 (mtt-85) REVERT: D 181 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: D 182 ARG cc_start: 0.8226 (ttp80) cc_final: 0.8024 (mtp-110) REVERT: D 290 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: D 357 LYS cc_start: 0.8063 (tppt) cc_final: 0.7673 (tttt) REVERT: E 120 ASP cc_start: 0.7297 (p0) cc_final: 0.6932 (p0) REVERT: E 121 HIS cc_start: 0.7905 (p90) cc_final: 0.7499 (p90) REVERT: E 181 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: E 357 LYS cc_start: 0.8118 (tppt) cc_final: 0.7625 (ttpp) REVERT: F 64 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7656 (t0) REVERT: F 402 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: G 144 ARG cc_start: 0.8309 (mtt-85) cc_final: 0.7996 (mtp85) REVERT: H 120 ASP cc_start: 0.7275 (p0) cc_final: 0.6871 (p0) REVERT: H 181 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: H 326 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.7167 (mmt180) REVERT: H 375 LYS cc_start: 0.8279 (tptt) cc_final: 0.7987 (tptm) REVERT: I 64 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7744 (t0) REVERT: J 20 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8202 (ttmm) REVERT: J 144 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7979 (mtp85) REVERT: J 181 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8168 (pp20) REVERT: J 372 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7538 (mmt90) REVERT: K 120 ASP cc_start: 0.7318 (p0) cc_final: 0.6978 (p0) REVERT: K 403 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6816 (tttt) REVERT: L 64 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7666 (t0) REVERT: L 185 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: L 403 LYS cc_start: 0.7400 (ttpt) cc_final: 0.7188 (mtmm) outliers start: 92 outliers final: 29 residues processed: 521 average time/residue: 1.9296 time to fit residues: 1138.7266 Evaluate side-chains 482 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 438 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 50.0000 chunk 386 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 429 optimal weight: 0.7980 chunk 356 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 50.0000 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS B 314 GLN C 121 HIS C 314 GLN C 320 ASN C 388 GLN C 393 ASN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 314 GLN E 320 ASN E 393 ASN F 314 GLN F 320 ASN F 388 GLN F 393 ASN G 314 GLN G 388 GLN G 393 ASN H 388 GLN I 121 HIS I 388 GLN I 393 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32040 Z= 0.191 Angle : 0.496 4.354 43128 Z= 0.282 Chirality : 0.041 0.142 4764 Planarity : 0.003 0.042 5448 Dihedral : 5.462 178.597 4200 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.95 % Allowed : 11.87 % Favored : 86.18 % 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: 0.88 (0.14), residues: 3732 helix: 1.45 (0.12), residues: 2028 sheet: -0.07 (0.22), residues: 600 loop : -0.55 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 76 PHE 0.022 0.002 PHE K 269 TYR 0.024 0.002 TYR H 177 ARG 0.003 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 461 time to evaluate : 3.613 Fit side-chains REVERT: A 181 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: A 326 ARG cc_start: 0.7363 (mmt90) cc_final: 0.6967 (mmt180) REVERT: B 120 ASP cc_start: 0.7074 (p0) cc_final: 0.6686 (p0) REVERT: B 121 HIS cc_start: 0.7837 (p90) cc_final: 0.7408 (p-80) REVERT: C 120 ASP cc_start: 0.7292 (p0) cc_final: 0.6965 (p0) REVERT: C 144 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7868 (mtt-85) REVERT: C 375 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8242 (tptt) REVERT: C 399 MET cc_start: 0.6224 (ttp) cc_final: 0.5991 (tpt) REVERT: D 181 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: D 290 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: D 326 ARG cc_start: 0.7360 (mmt90) cc_final: 0.6940 (mmt-90) REVERT: E 120 ASP cc_start: 0.7307 (p0) cc_final: 0.6931 (p0) REVERT: E 121 HIS cc_start: 0.7888 (p90) cc_final: 0.7462 (p90) REVERT: E 181 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: E 388 GLN cc_start: 0.7119 (mt0) cc_final: 0.6849 (mt0) REVERT: F 64 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7618 (t0) REVERT: F 402 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: G 326 ARG cc_start: 0.7368 (mmt90) cc_final: 0.6977 (mmt180) REVERT: H 120 ASP cc_start: 0.7297 (p0) cc_final: 0.6895 (p0) REVERT: H 181 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: H 326 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.7168 (mmt180) REVERT: J 20 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: J 181 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: J 326 ARG cc_start: 0.7359 (mmt90) cc_final: 0.6936 (mmt-90) REVERT: J 372 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7887 (mmt90) REVERT: J 403 LYS cc_start: 0.7287 (ttpt) cc_final: 0.6975 (mtmm) REVERT: K 120 ASP cc_start: 0.7340 (p0) cc_final: 0.6999 (p0) REVERT: K 403 LYS cc_start: 0.7379 (ttpt) cc_final: 0.6816 (tttt) REVERT: L 64 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7740 (t0) REVERT: L 185 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: L 403 LYS cc_start: 0.7329 (ttpt) cc_final: 0.7098 (mtmm) outliers start: 68 outliers final: 26 residues processed: 504 average time/residue: 1.9647 time to fit residues: 1120.9038 Evaluate side-chains 476 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 438 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain H residue 185 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 389 SER Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 64 ASN Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 313 optimal weight: 0.0970 chunk 243 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 427 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN B 388 GLN C 121 HIS C 314 GLN C 388 GLN C 393 ASN D 388 GLN E 314 GLN E 388 GLN E 393 ASN F 314 GLN F 388 GLN F 393 ASN G 314 GLN G 388 GLN G 393 ASN I 121 HIS I 388 GLN I 393 ASN J 320 ASN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 32040 Z= 0.113 Angle : 0.405 4.132 43128 Z= 0.233 Chirality : 0.038 0.139 4764 Planarity : 0.003 0.035 5448 Dihedral : 5.074 179.598 4200 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.18 % Allowed : 12.79 % Favored : 86.03 % 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: 1.50 (0.14), residues: 3732 helix: 1.99 (0.12), residues: 2028 sheet: 0.09 (0.23), residues: 600 loop : -0.29 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 76 PHE 0.014 0.001 PHE E 189 TYR 0.018 0.001 TYR H 177 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 467 time to evaluate : 3.928 Fit side-chains REVERT: A 181 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: A 326 ARG cc_start: 0.7321 (mmt90) cc_final: 0.6959 (mmt180) REVERT: B 120 ASP cc_start: 0.7157 (p0) cc_final: 0.6772 (p0) REVERT: B 121 HIS cc_start: 0.7820 (p90) cc_final: 0.7429 (p90) REVERT: C 120 ASP cc_start: 0.7285 (p0) cc_final: 0.6946 (p0) REVERT: C 399 MET cc_start: 0.6283 (ttp) cc_final: 0.5971 (tpt) REVERT: C 406 SER cc_start: 0.7220 (m) cc_final: 0.6607 (t) REVERT: D 290 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: D 326 ARG cc_start: 0.7313 (mmt90) cc_final: 0.6950 (mmt180) REVERT: D 357 LYS cc_start: 0.8024 (tppt) cc_final: 0.7582 (tttt) REVERT: E 120 ASP cc_start: 0.7315 (p0) cc_final: 0.6928 (p0) REVERT: E 121 HIS cc_start: 0.7854 (p90) cc_final: 0.7399 (p90) REVERT: E 181 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: E 357 LYS cc_start: 0.8048 (tppt) cc_final: 0.7657 (tttp) REVERT: F 269 PHE cc_start: 0.8350 (t80) cc_final: 0.8113 (t80) REVERT: F 290 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: F 389 SER cc_start: 0.7283 (OUTLIER) cc_final: 0.6966 (m) REVERT: G 326 ARG cc_start: 0.7318 (mmt90) cc_final: 0.6963 (mmt180) REVERT: H 181 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: H 326 ARG cc_start: 0.7381 (mmt-90) cc_final: 0.6994 (mmt180) REVERT: I 269 PHE cc_start: 0.8369 (t80) cc_final: 0.8143 (t80) REVERT: J 181 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7880 (pp20) REVERT: J 326 ARG cc_start: 0.7315 (mmt90) cc_final: 0.6943 (mmt180) REVERT: J 372 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7103 (mmt90) REVERT: J 401 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.5860 (mmtp) REVERT: J 403 LYS cc_start: 0.7214 (ttpt) cc_final: 0.6900 (mtmm) REVERT: K 120 ASP cc_start: 0.7355 (p0) cc_final: 0.7014 (p0) REVERT: K 357 LYS cc_start: 0.7999 (tppt) cc_final: 0.7587 (tttm) REVERT: K 403 LYS cc_start: 0.7271 (ttpt) cc_final: 0.6712 (tttt) REVERT: L 144 ARG cc_start: 0.8239 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: L 290 GLU cc_start: 0.8010 (mp0) cc_final: 0.7776 (mm-30) REVERT: L 403 LYS cc_start: 0.7316 (ttpt) cc_final: 0.7080 (mtmm) REVERT: L 406 SER cc_start: 0.7103 (m) cc_final: 0.6512 (t) outliers start: 41 outliers final: 6 residues processed: 493 average time/residue: 1.9943 time to fit residues: 1115.5407 Evaluate side-chains 439 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 424 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 401 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 255 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 291 optimal weight: 50.0000 chunk 211 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN H 314 GLN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32040 Z= 0.206 Angle : 0.508 4.890 43128 Z= 0.288 Chirality : 0.041 0.139 4764 Planarity : 0.003 0.047 5448 Dihedral : 5.406 178.049 4200 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.35 % Allowed : 13.25 % Favored : 85.40 % 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: 1.14 (0.14), residues: 3732 helix: 1.66 (0.12), residues: 2028 sheet: 0.05 (0.23), residues: 600 loop : -0.42 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 76 PHE 0.025 0.002 PHE K 269 TYR 0.024 0.002 TYR L 177 ARG 0.007 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 451 time to evaluate : 4.119 Fit side-chains REVERT: A 326 ARG cc_start: 0.7417 (mmt90) cc_final: 0.7029 (mmt180) REVERT: A 372 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7651 (mmm160) REVERT: B 120 ASP cc_start: 0.7162 (p0) cc_final: 0.6793 (p0) REVERT: B 121 HIS cc_start: 0.7825 (p90) cc_final: 0.7468 (p90) REVERT: B 144 ARG cc_start: 0.8216 (mtt-85) cc_final: 0.7907 (mtt-85) REVERT: C 120 ASP cc_start: 0.7285 (p0) cc_final: 0.6955 (p0) REVERT: C 406 SER cc_start: 0.7247 (m) cc_final: 0.6647 (t) REVERT: D 290 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: D 326 ARG cc_start: 0.7391 (mmt90) cc_final: 0.6993 (mmt180) REVERT: D 357 LYS cc_start: 0.7998 (tppt) cc_final: 0.7654 (tttm) REVERT: E 120 ASP cc_start: 0.7306 (p0) cc_final: 0.6929 (p0) REVERT: E 121 HIS cc_start: 0.7896 (p90) cc_final: 0.7424 (p90) REVERT: E 181 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: G 326 ARG cc_start: 0.7398 (mmt90) cc_final: 0.7010 (mmt180) REVERT: G 341 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7955 (tt0) REVERT: G 357 LYS cc_start: 0.8060 (tppt) cc_final: 0.7700 (tttm) REVERT: H 120 ASP cc_start: 0.7318 (p0) cc_final: 0.6942 (p0) REVERT: H 181 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: H 326 ARG cc_start: 0.7495 (mmt-90) cc_final: 0.7180 (mmt180) REVERT: J 326 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7013 (mmt180) REVERT: J 372 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7823 (mmt90) REVERT: J 401 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5872 (mmtp) REVERT: J 403 LYS cc_start: 0.7260 (ttpt) cc_final: 0.7040 (mtmm) REVERT: K 120 ASP cc_start: 0.7361 (p0) cc_final: 0.7004 (p0) REVERT: K 403 LYS cc_start: 0.7375 (ttpt) cc_final: 0.6824 (tttt) REVERT: L 185 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: L 403 LYS cc_start: 0.7405 (ttpt) cc_final: 0.7138 (mtmm) REVERT: L 406 SER cc_start: 0.7186 (m) cc_final: 0.6585 (t) outliers start: 47 outliers final: 13 residues processed: 484 average time/residue: 1.9378 time to fit residues: 1063.4841 Evaluate side-chains 457 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 437 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 389 SER Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 3.9990 chunk 409 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 398 optimal weight: 5.9990 chunk 240 optimal weight: 0.4980 chunk 173 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 360 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 397 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 388 GLN C 121 HIS C 314 GLN C 320 ASN C 393 ASN D 314 GLN E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32040 Z= 0.219 Angle : 0.526 6.089 43128 Z= 0.296 Chirality : 0.042 0.141 4764 Planarity : 0.004 0.045 5448 Dihedral : 5.482 178.175 4200 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.55 % Allowed : 12.82 % Favored : 85.63 % 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: 0.97 (0.14), residues: 3732 helix: 1.50 (0.12), residues: 2028 sheet: 0.01 (0.22), residues: 600 loop : -0.49 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 76 PHE 0.026 0.002 PHE K 269 TYR 0.025 0.002 TYR L 177 ARG 0.006 0.001 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 442 time to evaluate : 3.899 Fit side-chains REVERT: A 326 ARG cc_start: 0.7406 (mmt90) cc_final: 0.7019 (mmt180) REVERT: B 120 ASP cc_start: 0.7162 (p0) cc_final: 0.6790 (p0) REVERT: B 121 HIS cc_start: 0.7855 (p90) cc_final: 0.7489 (p90) REVERT: B 144 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7924 (mtt-85) REVERT: B 181 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7502 (tp30) REVERT: B 388 GLN cc_start: 0.7150 (mt0) cc_final: 0.6915 (mt0) REVERT: C 120 ASP cc_start: 0.7277 (p0) cc_final: 0.6931 (p0) REVERT: C 406 SER cc_start: 0.7275 (m) cc_final: 0.6659 (t) REVERT: D 290 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: D 326 ARG cc_start: 0.7402 (mmt90) cc_final: 0.6993 (mmt180) REVERT: D 357 LYS cc_start: 0.7995 (tppt) cc_final: 0.7716 (tttt) REVERT: E 120 ASP cc_start: 0.7296 (p0) cc_final: 0.6910 (p0) REVERT: E 121 HIS cc_start: 0.7919 (p90) cc_final: 0.7408 (p90) REVERT: E 181 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: F 403 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7471 (mtmm) REVERT: G 326 ARG cc_start: 0.7423 (mmt90) cc_final: 0.7020 (mmt180) REVERT: G 341 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7966 (mt-10) REVERT: G 357 LYS cc_start: 0.8044 (tppt) cc_final: 0.7665 (tttm) REVERT: H 120 ASP cc_start: 0.7294 (p0) cc_final: 0.6858 (p0) REVERT: H 121 HIS cc_start: 0.7883 (p-80) cc_final: 0.7530 (p90) REVERT: H 181 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: H 326 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.7255 (mmt180) REVERT: J 181 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7939 (pp20) REVERT: J 185 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: J 326 ARG cc_start: 0.7403 (mmt90) cc_final: 0.7008 (mmt180) REVERT: J 372 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7838 (mmt90) REVERT: J 401 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5862 (mmtp) REVERT: K 120 ASP cc_start: 0.7278 (p0) cc_final: 0.6934 (p0) REVERT: K 403 LYS cc_start: 0.7303 (ttpt) cc_final: 0.6758 (tttt) REVERT: L 185 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: L 403 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7180 (mtmm) REVERT: L 406 SER cc_start: 0.7230 (m) cc_final: 0.6611 (t) outliers start: 54 outliers final: 24 residues processed: 479 average time/residue: 1.9492 time to fit residues: 1058.7244 Evaluate side-chains 473 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 439 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 102 ILE Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 389 SER Chi-restraints excluded: chain J residue 401 LYS Chi-restraints excluded: chain L residue 57 ARG Chi-restraints excluded: chain L residue 102 ILE Chi-restraints excluded: chain L residue 185 GLU Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 0.0370 chunk 421 optimal weight: 0.8980 chunk 257 optimal weight: 50.0000 chunk 200 optimal weight: 7.9990 chunk 293 optimal weight: 50.0000 chunk 442 optimal weight: 50.0000 chunk 407 optimal weight: 0.6980 chunk 352 optimal weight: 1.9990 chunk 36 optimal weight: 50.0000 chunk 272 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32040 Z= 0.155 Angle : 0.465 6.900 43128 Z= 0.264 Chirality : 0.039 0.137 4764 Planarity : 0.003 0.035 5448 Dihedral : 5.290 178.959 4200 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.06 % Allowed : 13.45 % Favored : 85.49 % 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: 1.26 (0.14), residues: 3732 helix: 1.76 (0.12), residues: 2028 sheet: 0.07 (0.23), residues: 600 loop : -0.36 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.018 0.001 PHE K 269 TYR 0.022 0.001 TYR K 177 ARG 0.005 0.000 ARG H 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 440 time to evaluate : 3.642 Fit side-chains REVERT: A 326 ARG cc_start: 0.7381 (mmt90) cc_final: 0.6991 (mmt180) REVERT: B 120 ASP cc_start: 0.7166 (p0) cc_final: 0.6785 (p0) REVERT: B 121 HIS cc_start: 0.7826 (p90) cc_final: 0.7443 (p90) REVERT: B 144 ARG cc_start: 0.8212 (mtt-85) cc_final: 0.7924 (mtt-85) REVERT: B 181 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: C 120 ASP cc_start: 0.7309 (p0) cc_final: 0.6955 (p0) REVERT: C 403 LYS cc_start: 0.7540 (mtmm) cc_final: 0.7213 (mtmm) REVERT: C 406 SER cc_start: 0.7240 (m) cc_final: 0.6621 (t) REVERT: D 290 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: D 326 ARG cc_start: 0.7362 (mmt90) cc_final: 0.6966 (mmt180) REVERT: D 357 LYS cc_start: 0.7989 (tppt) cc_final: 0.7656 (tttm) REVERT: E 120 ASP cc_start: 0.7295 (p0) cc_final: 0.6910 (p0) REVERT: E 121 HIS cc_start: 0.7936 (p90) cc_final: 0.7406 (p90) REVERT: E 181 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: E 403 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7387 (mtpt) REVERT: F 403 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7420 (mtmm) REVERT: G 326 ARG cc_start: 0.7379 (mmt90) cc_final: 0.6990 (mmt180) REVERT: G 341 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7862 (tt0) REVERT: G 357 LYS cc_start: 0.8075 (tppt) cc_final: 0.7694 (tttm) REVERT: H 120 ASP cc_start: 0.7302 (p0) cc_final: 0.6873 (p0) REVERT: H 121 HIS cc_start: 0.7838 (p-80) cc_final: 0.7425 (p-80) REVERT: H 181 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: H 326 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.7194 (mmt180) REVERT: I 269 PHE cc_start: 0.8472 (t80) cc_final: 0.8266 (t80) REVERT: I 290 GLU cc_start: 0.8162 (mp0) cc_final: 0.7885 (mm-30) REVERT: J 181 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: J 185 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: J 326 ARG cc_start: 0.7376 (mmt90) cc_final: 0.6996 (mmt180) REVERT: J 372 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7046 (mtt180) REVERT: K 120 ASP cc_start: 0.7271 (p0) cc_final: 0.6933 (p0) REVERT: K 403 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6754 (tttt) REVERT: L 290 GLU cc_start: 0.8116 (mp0) cc_final: 0.7871 (mm-30) REVERT: L 403 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7156 (mtmm) REVERT: L 406 SER cc_start: 0.7226 (m) cc_final: 0.6603 (t) outliers start: 37 outliers final: 15 residues processed: 466 average time/residue: 1.8929 time to fit residues: 1000.5938 Evaluate side-chains 458 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 435 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 181 GLU Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 389 SER Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 389 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 1.9990 chunk 375 optimal weight: 0.9990 chunk 107 optimal weight: 50.0000 chunk 324 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 352 optimal weight: 0.8980 chunk 147 optimal weight: 50.0000 chunk 362 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 314 GLN C 121 HIS C 314 GLN C 393 ASN D 314 GLN E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN F 393 ASN G 314 GLN G 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118203 restraints weight = 32152.840| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.17 r_work: 0.3148 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 32040 Z= 0.159 Angle : 0.471 9.008 43128 Z= 0.267 Chirality : 0.040 0.137 4764 Planarity : 0.003 0.041 5448 Dihedral : 5.285 178.735 4200 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.18 % Allowed : 13.22 % Favored : 85.60 % 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: 1.27 (0.14), residues: 3732 helix: 1.76 (0.12), residues: 2028 sheet: 0.09 (0.23), residues: 600 loop : -0.35 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 76 PHE 0.018 0.001 PHE K 269 TYR 0.022 0.001 TYR H 177 ARG 0.009 0.000 ARG H 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16135.24 seconds wall clock time: 283 minutes 37.84 seconds (17017.84 seconds total)