Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 03:12:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/08_2023/8pho_17669.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/08_2023/8pho_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_17669/08_2023/8pho_17669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/08_2023/8pho_17669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/08_2023/8pho_17669.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pho_17669/08_2023/8pho_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-1.21rc1-5044/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: 15.10, per 1000 atoms: 0.47 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: 11.54 Conformation dependent library (CDL) restraints added in 4.3 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: 2.93 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: 10.53 Time building geometry restraints manager: 12.52 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.010 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 74.150 Find NCS groups from input model: 2.040 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: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.180 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 696 average time/residue: 2.0236 time to fit residues: 1589.1580 Evaluate side-chains 484 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 3.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2009 ------------------------------------------------------------------------------- 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: 0.0970 chunk 134 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 chunk 403 optimal weight: 50.0000 overall best weight: 0.4206 ------------------------------------------------------------------------------- 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 368 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 337 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 E 388 GLN 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 K 320 ASN L 187 HIS L 312 ASN ** L 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.186 32040 Z= 0.444 Angle : 1.345 33.135 43128 Z= 0.700 Chirality : 0.068 0.782 4764 Planarity : 0.019 0.437 5448 Dihedral : 6.128 132.733 4200 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.20 % Favored : 97.59 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.47 (0.12), residues: 3732 helix: -0.72 (0.11), residues: 2004 sheet: -0.95 (0.20), residues: 624 loop : -1.07 (0.16), residues: 1104 *********************** 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 694 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 580 time to evaluate : 4.004 Fit side-chains outliers start: 114 outliers final: 12 residues processed: 629 average time/residue: 2.0520 time to fit residues: 1459.9097 Evaluate side-chains 463 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 451 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 5 average time/residue: 0.3055 time to fit residues: 8.2248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 224 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 335 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 403 optimal weight: 50.0000 chunk 436 optimal weight: 1.9990 chunk 359 optimal weight: 0.8980 chunk 400 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 324 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 B 388 GLN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 314 GLN F 339 GLN F 388 GLN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 32040 Z= 0.148 Angle : 0.470 4.991 43128 Z= 0.268 Chirality : 0.040 0.141 4764 Planarity : 0.004 0.054 5448 Dihedral : 5.043 173.576 4200 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 1.95 % 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: 0.65 (0.14), residues: 3732 helix: 1.31 (0.12), residues: 2016 sheet: -0.33 (0.21), residues: 600 loop : -0.61 (0.17), residues: 1116 *********************** 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 580 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 512 time to evaluate : 4.150 Fit side-chains outliers start: 68 outliers final: 13 residues processed: 550 average time/residue: 2.1336 time to fit residues: 1322.8321 Evaluate side-chains 464 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 451 time to evaluate : 4.119 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 5 residues processed: 8 average time/residue: 0.5693 time to fit residues: 12.0212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 399 optimal weight: 0.6980 chunk 303 optimal weight: 9.9990 chunk 209 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 192 optimal weight: 0.0470 chunk 271 optimal weight: 8.9990 chunk 405 optimal weight: 50.0000 chunk 429 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 384 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 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 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN E 314 GLN F 314 GLN F 388 GLN G 121 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 GLN L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 32040 Z= 0.114 Angle : 0.410 3.886 43128 Z= 0.235 Chirality : 0.038 0.133 4764 Planarity : 0.003 0.042 5448 Dihedral : 4.842 179.197 4200 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer Outliers : 0.95 % 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: 1.41 (0.14), residues: 3732 helix: 2.02 (0.12), residues: 2016 sheet: -0.20 (0.21), residues: 600 loop : -0.36 (0.17), residues: 1116 *********************** 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 508 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 475 time to evaluate : 4.019 Fit side-chains outliers start: 33 outliers final: 4 residues processed: 496 average time/residue: 2.0768 time to fit residues: 1161.1651 Evaluate side-chains 421 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 417 time to evaluate : 3.847 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 5.0732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 357 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 366 optimal weight: 50.0000 chunk 296 optimal weight: 6.9990 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: 3.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 94 GLN D 121 HIS D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 GLN F 314 GLN F 320 ASN G 121 HIS G 187 HIS G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 GLN ** H 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN I 314 GLN I 320 ASN I 393 ASN J 94 GLN 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 187 HIS L 312 ASN L 314 GLN L 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 32040 Z= 0.299 Angle : 0.607 6.414 43128 Z= 0.339 Chirality : 0.045 0.159 4764 Planarity : 0.004 0.062 5448 Dihedral : 5.522 177.333 4200 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3732 helix: 1.42 (0.12), residues: 2016 sheet: -0.07 (0.22), residues: 600 loop : -0.61 (0.16), residues: 1116 *********************** 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 543 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 466 time to evaluate : 3.937 Fit side-chains outliers start: 77 outliers final: 18 residues processed: 508 average time/residue: 1.9980 time to fit residues: 1151.1914 Evaluate side-chains 439 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 421 time to evaluate : 4.173 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 7 residues processed: 11 average time/residue: 0.2783 time to fit residues: 11.0452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 144 optimal weight: 50.0000 chunk 386 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 429 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 35 optimal weight: 50.0000 chunk 142 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 320 ASN C 388 GLN C 393 ASN D 121 HIS D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 GLN E 320 ASN E 388 GLN F 314 GLN F 320 ASN G 121 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 I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN L 121 HIS L 314 GLN L 320 ASN L 388 GLN L 393 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 32040 Z= 0.298 Angle : 0.600 5.801 43128 Z= 0.336 Chirality : 0.045 0.144 4764 Planarity : 0.004 0.053 5448 Dihedral : 5.725 176.399 4200 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer Outliers : 2.04 % 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: 0.50 (0.14), residues: 3732 helix: 1.17 (0.12), residues: 2016 sheet: -0.31 (0.22), residues: 624 loop : -0.71 (0.16), residues: 1092 *********************** 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 514 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 443 time to evaluate : 3.651 Fit side-chains outliers start: 71 outliers final: 30 residues processed: 493 average time/residue: 2.0087 time to fit residues: 1121.8640 Evaluate side-chains 454 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 424 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 10 average time/residue: 0.2768 time to fit residues: 10.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 414 optimal weight: 0.0870 chunk 48 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 361 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 427 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 314 GLN C 320 ASN C 388 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 121 HIS E 320 ASN F 121 HIS F 314 GLN G 314 GLN G 393 ASN H 314 GLN H 388 GLN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 320 ASN L 121 HIS L 314 GLN L 388 GLN L 393 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 32040 Z= 0.174 Angle : 0.481 4.210 43128 Z= 0.275 Chirality : 0.040 0.142 4764 Planarity : 0.003 0.042 5448 Dihedral : 5.440 178.839 4200 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3732 helix: 1.56 (0.12), residues: 2028 sheet: 0.01 (0.23), residues: 600 loop : -0.50 (0.17), residues: 1104 *********************** 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 505 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 456 time to evaluate : 4.040 Fit side-chains outliers start: 49 outliers final: 18 residues processed: 496 average time/residue: 2.0330 time to fit residues: 1144.3675 Evaluate side-chains 451 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 433 time to evaluate : 3.988 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.2909 time to fit residues: 5.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 50.0000 chunk 128 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 291 optimal weight: 50.0000 chunk 211 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 314 GLN C 320 ASN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 314 GLN E 320 ASN E 388 GLN F 121 HIS F 314 GLN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** K 320 ASN 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: 0.8401 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 32040 Z= 0.240 Angle : 0.550 11.049 43128 Z= 0.310 Chirality : 0.043 0.150 4764 Planarity : 0.004 0.044 5448 Dihedral : 5.615 177.712 4200 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.55 % 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: 0.79 (0.14), residues: 3732 helix: 1.35 (0.12), residues: 2028 sheet: -0.05 (0.22), residues: 600 loop : -0.58 (0.16), residues: 1104 *********************** 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 483 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 429 time to evaluate : 4.173 Fit side-chains outliers start: 54 outliers final: 27 residues processed: 469 average time/residue: 2.0093 time to fit residues: 1071.7576 Evaluate side-chains 455 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 428 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 8 average time/residue: 0.2906 time to fit residues: 9.5628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 389 optimal weight: 4.9990 chunk 409 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 398 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 377 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 314 GLN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 314 GLN E 320 ASN E 393 ASN F 121 HIS F 314 GLN G 314 GLN G 393 ASN H 314 GLN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN K 320 ASN L 121 HIS 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: 0.8377 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 32040 Z= 0.168 Angle : 0.482 9.526 43128 Z= 0.274 Chirality : 0.040 0.143 4764 Planarity : 0.003 0.039 5448 Dihedral : 5.419 178.888 4200 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer Outliers : 1.15 % 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: 1.12 (0.14), residues: 3732 helix: 1.65 (0.12), residues: 2028 sheet: -0.01 (0.22), residues: 600 loop : -0.43 (0.17), residues: 1104 *********************** 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 477 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 437 time to evaluate : 4.237 Fit side-chains outliers start: 40 outliers final: 22 residues processed: 470 average time/residue: 2.0056 time to fit residues: 1070.1798 Evaluate side-chains 451 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 429 time to evaluate : 3.860 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.2852 time to fit residues: 6.7697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 261 optimal weight: 6.9990 chunk 421 optimal weight: 5.9990 chunk 257 optimal weight: 50.0000 chunk 200 optimal weight: 4.9990 chunk 293 optimal weight: 50.0000 chunk 442 optimal weight: 50.0000 chunk 407 optimal weight: 5.9990 chunk 352 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 272 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 314 GLN C 320 ASN C 393 ASN D 314 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 ASN E 314 GLN E 320 ASN E 359 ASN E 393 ASN F 121 HIS F 314 GLN F 320 ASN G 314 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 ASN H 314 GLN H 393 ASN I 121 HIS I 314 GLN I 393 ASN J 314 GLN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN L 121 HIS L 314 GLN ** L 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 32040 Z= 0.371 Angle : 0.667 11.491 43128 Z= 0.369 Chirality : 0.047 0.211 4764 Planarity : 0.005 0.070 5448 Dihedral : 5.861 175.723 4200 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 1.18 % 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: 0.35 (0.13), residues: 3732 helix: 1.03 (0.12), residues: 2016 sheet: -0.33 (0.22), residues: 624 loop : -0.77 (0.16), residues: 1092 ********************** 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 473 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 432 time to evaluate : 4.016 Fit side-chains outliers start: 41 outliers final: 23 residues processed: 463 average time/residue: 1.9491 time to fit residues: 1029.5401 Evaluate side-chains 445 residues out of total 3480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 422 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 7 average time/residue: 0.6305 time to fit residues: 11.5550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 279 optimal weight: 0.9980 chunk 375 optimal weight: 0.9980 chunk 107 optimal weight: 50.0000 chunk 324 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 352 optimal weight: 4.9990 chunk 147 optimal weight: 50.0000 chunk 362 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 64 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 314 GLN C 388 GLN C 393 ASN D 314 GLN D 393 ASN E 314 GLN E 393 ASN F 121 HIS F 314 GLN G 314 GLN G 393 ASN H 314 GLN H 393 ASN I 121 HIS I 314 GLN I 393 ASN L 121 HIS L 314 GLN L 393 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.119549 restraints weight = 32074.237| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.18 r_work: 0.3167 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 32040 Z= 0.140 Angle : 0.458 8.592 43128 Z= 0.261 Chirality : 0.039 0.151 4764 Planarity : 0.003 0.037 5448 Dihedral : 5.363 179.305 4200 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer Outliers : 0.75 % 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: 1.21 (0.14), residues: 3732 helix: 1.73 (0.12), residues: 2028 sheet: 0.03 (0.23), residues: 600 loop : -0.40 (0.17), residues: 1104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16074.71 seconds wall clock time: 284 minutes 16.22 seconds (17056.22 seconds total)