Starting phenix.real_space_refine on Mon Mar 18 08:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rja_4901/03_2024/6rja_4901.pdb" } resolution = 3.0 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= 0.011 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: 5 Type Number sf(0) Gaussians P 194 5.49 5 S 50 5.16 5 C 12214 2.51 5 N 3522 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C ASP 330": "OD1" <-> "OD2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ASP 859": "OD1" <-> "OD2" Residue "C ARG 876": "NH1" <-> "NH2" Residue "C GLU 883": "OE1" <-> "OE2" Residue "C GLU 887": "OE1" <-> "OE2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C ASP 939": "OD1" <-> "OD2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 1002": "OE1" <-> "OE2" Residue "C ASP 1014": "OD1" <-> "OD2" Residue "C PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1120": "OD1" <-> "OD2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 46": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F ASP 283": "OD1" <-> "OD2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F ASP 330": "OD1" <-> "OD2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 390": "OE1" <-> "OE2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 413": "NH1" <-> "NH2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 502": "OD1" <-> "OD2" Residue "F ARG 703": "NH1" <-> "NH2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F ARG 831": "NH1" <-> "NH2" Residue "F ASP 859": "OD1" <-> "OD2" Residue "F ARG 876": "NH1" <-> "NH2" Residue "F GLU 883": "OE1" <-> "OE2" Residue "F GLU 887": "OE1" <-> "OE2" Residue "F GLU 916": "OE1" <-> "OE2" Residue "F ARG 921": "NH1" <-> "NH2" Residue "F ASP 939": "OD1" <-> "OD2" Residue "F ARG 966": "NH1" <-> "NH2" Residue "F GLU 1002": "OE1" <-> "OE2" Residue "F ASP 1014": "OD1" <-> "OD2" Residue "F PHE 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1120": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20372 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6638 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 795} Chain breaks: 7 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 6638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6638 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 795} Chain breaks: 7 Chain: "G" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "H" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 10.61, per 1000 atoms: 0.52 Number of scatterers: 20372 At special positions: 0 Unit cell: (120.015, 207.137, 107.569, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 194 15.00 O 4392 8.00 N 3522 7.00 C 12214 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: 8.71 Conformation dependent library (CDL) restraints added in 2.9 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3736 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 45.6% alpha, 13.8% beta 64 base pairs and 115 stacking pairs defined. Time for finding SS restraints: 7.33 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.774A pdb=" N LYS A 50 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 51 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.541A pdb=" N VAL A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.782A pdb=" N ALA A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.544A pdb=" N TYR A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 178 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.775A pdb=" N LYS B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET B 51 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.540A pdb=" N VAL B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.781A pdb=" N ALA B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.545A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.543A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.813A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.007A pdb=" N ILE C 254 " --> pdb=" O ILE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.623A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 384 through 395 Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL C 406 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 454 Processing helix chain 'C' and resid 470 through 476 Processing helix chain 'C' and resid 479 through 500 Processing helix chain 'C' and resid 692 through 705 Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR C 858 " --> pdb=" O THR C 854 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 859 " --> pdb=" O GLN C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 871 No H-bonds generated for 'chain 'C' and resid 869 through 871' Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.772A pdb=" N ARG C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 891 Proline residue: C 888 - end of helix removed outlier: 3.717A pdb=" N GLU C 891 " --> pdb=" O GLU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 removed outlier: 3.502A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.544A pdb=" N LEU F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.634A pdb=" N HIS F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 185 through 204 removed outlier: 3.814A pdb=" N TYR F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.006A pdb=" N ILE F 254 " --> pdb=" O ILE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 285 removed outlier: 3.624A pdb=" N GLN F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 315 through 327 removed outlier: 3.940A pdb=" N LEU F 327 " --> pdb=" O ILE F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 Processing helix chain 'F' and resid 369 through 382 Processing helix chain 'F' and resid 384 through 395 Processing helix chain 'F' and resid 402 through 416 removed outlier: 3.812A pdb=" N VAL F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 436 Processing helix chain 'F' and resid 445 through 454 Processing helix chain 'F' and resid 470 through 476 Processing helix chain 'F' and resid 479 through 500 Processing helix chain 'F' and resid 692 through 705 Processing helix chain 'F' and resid 737 through 748 Processing helix chain 'F' and resid 854 through 868 removed outlier: 3.798A pdb=" N TYR F 858 " --> pdb=" O THR F 854 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP F 859 " --> pdb=" O GLN F 855 " (cutoff:3.500A) Processing helix chain 'F' and resid 869 through 871 No H-bonds generated for 'chain 'F' and resid 869 through 871' Processing helix chain 'F' and resid 872 through 878 removed outlier: 3.771A pdb=" N ARG F 876 " --> pdb=" O PHE F 872 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 891 Proline residue: F 888 - end of helix removed outlier: 3.717A pdb=" N GLU F 891 " --> pdb=" O GLU F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 910 through 918 Processing helix chain 'F' and resid 986 through 988 No H-bonds generated for 'chain 'F' and resid 986 through 988' Processing helix chain 'F' and resid 1000 through 1011 removed outlier: 3.503A pdb=" N TYR F1004 " --> pdb=" O SER F1000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 6.634A pdb=" N ILE B 115 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 136 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 117 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 134 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY B 119 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET B 121 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA B 130 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.648A pdb=" N SER B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 710 through 712 removed outlier: 3.764A pdb=" N ILE C 10 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 172 Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU C 935 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 958 " --> pdb=" O TYR C 828 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 972 " --> pdb=" O LYS C 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA C 967 " --> pdb=" O THR C1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C1022 " --> pdb=" O ALA C 967 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 969 " --> pdb=" O LYS C1020 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB3, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C1098 " --> pdb=" O ILE C1110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 710 through 712 removed outlier: 3.765A pdb=" N ILE F 10 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 168 through 172 Processing sheet with id=AB6, first strand: chain 'F' and resid 268 through 269 removed outlier: 3.746A pdb=" N ALA F 268 " --> pdb=" O HIS F 425 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 935 through 941 removed outlier: 3.509A pdb=" N LEU F 935 " --> pdb=" O ILE F 849 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL F 845 " --> pdb=" O ASP F 939 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS F 941 " --> pdb=" O THR F 843 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR F 843 " --> pdb=" O LYS F 941 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA F 829 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 958 " --> pdb=" O TYR F 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU F 983 " --> pdb=" O TRP F 965 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 977 through 980 removed outlier: 3.833A pdb=" N LYS F 977 " --> pdb=" O ASN F 972 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 972 " --> pdb=" O LYS F 977 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA F 967 " --> pdb=" O THR F1022 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR F1022 " --> pdb=" O ALA F 967 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL F 969 " --> pdb=" O LYS F1020 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 989 through 990 Processing sheet with id=AC2, first strand: chain 'F' and resid 1085 through 1088 removed outlier: 4.273A pdb=" N CYS F1085 " --> pdb=" O LEU F1058 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU F1057 " --> pdb=" O LEU F1045 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU F1028 " --> pdb=" O VAL F1099 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F1098 " --> pdb=" O ILE F1110 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 115 stacking parallelities Total time for adding SS restraints: 8.64 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4442 1.33 - 1.45: 5508 1.45 - 1.57: 10714 1.57 - 1.69: 380 1.69 - 1.81: 92 Bond restraints: 21136 Sorted by residual: bond pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta sigma weight residual 1.464 1.485 -0.021 1.23e-02 6.61e+03 2.89e+00 bond pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta sigma weight residual 1.464 1.485 -0.021 1.23e-02 6.61e+03 2.87e+00 bond pdb=" C GLU C 887 " pdb=" N PRO C 888 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.28e+00 bond pdb=" C GLU F 887 " pdb=" N PRO F 888 " ideal model delta sigma weight residual 1.335 1.356 -0.020 1.36e-02 5.41e+03 2.20e+00 bond pdb=" CA GLU F 887 " pdb=" C GLU F 887 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.14e+00 ... (remaining 21131 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.69: 1421 106.69 - 113.57: 11600 113.57 - 120.44: 8546 120.44 - 127.31: 7271 127.31 - 134.19: 464 Bond angle restraints: 29302 Sorted by residual: angle pdb=" C ASN C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C ASN F 21 " pdb=" N LYS F 22 " pdb=" CA LYS F 22 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" CA THR A 123 " pdb=" CB THR A 123 " pdb=" CG2 THR A 123 " ideal model delta sigma weight residual 110.50 116.77 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" CA TYR B 26 " pdb=" CB TYR B 26 " pdb=" CG TYR B 26 " ideal model delta sigma weight residual 113.90 120.53 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" CA THR B 123 " pdb=" CB THR B 123 " pdb=" CG2 THR B 123 " ideal model delta sigma weight residual 110.50 116.76 -6.26 1.70e+00 3.46e-01 1.36e+01 ... (remaining 29297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10987 17.76 - 35.51: 1358 35.51 - 53.27: 337 53.27 - 71.03: 178 71.03 - 88.78: 40 Dihedral angle restraints: 12900 sinusoidal: 7074 harmonic: 5826 Sorted by residual: dihedral pdb=" CA GLN C1052 " pdb=" C GLN C1052 " pdb=" N LYS C1053 " pdb=" CA LYS C1053 " ideal model delta harmonic sigma weight residual -180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLN F1052 " pdb=" C GLN F1052 " pdb=" N LYS F1053 " pdb=" CA LYS F1053 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLU C 384 " pdb=" C GLU C 384 " pdb=" N ARG C 385 " pdb=" CA ARG C 385 " ideal model delta harmonic sigma weight residual -180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 12897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2397 0.050 - 0.100: 743 0.100 - 0.149: 151 0.149 - 0.199: 22 0.199 - 0.249: 5 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1' U D 7 " pdb=" O4' U D 7 " pdb=" C2' U D 7 " pdb=" N1 U D 7 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1' U G 7 " pdb=" O4' U G 7 " pdb=" C2' U G 7 " pdb=" N1 U G 7 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1' A G 68 " pdb=" O4' A G 68 " pdb=" C2' A G 68 " pdb=" N9 A G 68 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3315 not shown) Planarity restraints: 3048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U G 7 " 0.033 2.00e-02 2.50e+03 1.84e-02 7.62e+00 pdb=" N1 U G 7 " -0.043 2.00e-02 2.50e+03 pdb=" C2 U G 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U G 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U G 7 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U G 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U G 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U G 7 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " -0.032 2.00e-02 2.50e+03 1.83e-02 7.54e+00 pdb=" N1 U D 7 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U D 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U D 7 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U D 7 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 150 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO C 151 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " -0.034 5.00e-02 4.00e+02 ... (remaining 3045 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6071 2.83 - 3.35: 15898 3.35 - 3.87: 33821 3.87 - 4.38: 40115 4.38 - 4.90: 64548 Nonbonded interactions: 160453 Sorted by model distance: nonbonded pdb=" O SER F 101 " pdb=" OG SER F 101 " model vdw 2.314 2.440 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 101 " model vdw 2.314 2.440 nonbonded pdb=" OH TYR F 225 " pdb=" OG1 THR F 383 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR C 225 " pdb=" OG1 THR C 383 " model vdw 2.320 2.440 nonbonded pdb=" O ALA F 376 " pdb=" OG1 THR F 380 " model vdw 2.351 2.440 ... (remaining 160448 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' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } 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: 2.330 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: 12.370 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 58.850 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 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:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 0.053 21136 Z= 0.340 Angle : 0.857 9.496 29302 Z= 0.471 Chirality : 0.050 0.249 3318 Planarity : 0.006 0.061 3048 Dihedral : 17.282 88.785 9164 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.23 % Allowed : 8.09 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.15), residues: 1960 helix: -1.92 (0.14), residues: 814 sheet: -0.73 (0.33), residues: 234 loop : -3.18 (0.15), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 424 HIS 0.014 0.002 HIS C 877 PHE 0.020 0.003 PHE F1042 TYR 0.029 0.002 TYR A 26 ARG 0.006 0.001 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 289 time to evaluate : 1.974 Fit side-chains REVERT: A 105 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8123 (ttpp) REVERT: B 40 LYS cc_start: 0.8055 (mttt) cc_final: 0.7850 (mttm) REVERT: B 105 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7975 (tttp) REVERT: C 314 MET cc_start: 0.5047 (tpt) cc_final: 0.4280 (mtp) REVERT: C 355 LYS cc_start: 0.7583 (tptt) cc_final: 0.7027 (tptp) REVERT: C 412 PHE cc_start: 0.7510 (t80) cc_final: 0.7294 (t80) REVERT: C 844 TYR cc_start: 0.7876 (m-80) cc_final: 0.7545 (m-80) REVERT: C 1010 LYS cc_start: 0.8312 (tptt) cc_final: 0.7939 (ttmt) REVERT: C 1038 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6361 (mt-10) REVERT: F 314 MET cc_start: 0.4953 (tpt) cc_final: 0.4296 (mtp) REVERT: F 355 LYS cc_start: 0.7728 (tptt) cc_final: 0.7176 (tptp) REVERT: F 844 TYR cc_start: 0.7915 (m-80) cc_final: 0.7657 (m-80) REVERT: F 1010 LYS cc_start: 0.8220 (tptt) cc_final: 0.7811 (ttmt) REVERT: F 1038 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6344 (mt-10) REVERT: F 1111 LYS cc_start: 0.7624 (tppt) cc_final: 0.6928 (tttt) outliers start: 4 outliers final: 1 residues processed: 291 average time/residue: 1.2598 time to fit residues: 415.3401 Evaluate side-chains 197 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 282 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 101 GLN A 127 ASN A 177 ASN B 37 ASN B 78 ASN B 101 GLN B 127 ASN B 177 ASN C 31 ASN C 49 ASN C 231 ASN C 279 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 303 GLN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1039 GLN C1081 ASN C1112 ASN F 31 ASN F 49 ASN F 231 ASN F 279 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 302 ASN F 303 GLN F 310 ASN ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F1039 GLN F1081 ASN F1112 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21136 Z= 0.212 Angle : 0.550 6.713 29302 Z= 0.297 Chirality : 0.038 0.145 3318 Planarity : 0.004 0.041 3048 Dihedral : 16.648 74.592 4984 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.83 % Allowed : 14.65 % Favored : 82.52 % 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: -1.93 (0.17), residues: 1960 helix: 0.01 (0.17), residues: 824 sheet: -0.85 (0.31), residues: 258 loop : -2.74 (0.16), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 38 HIS 0.004 0.001 HIS C 425 PHE 0.015 0.001 PHE F 412 TYR 0.025 0.002 TYR F 307 ARG 0.005 0.000 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 1.613 Fit side-chains REVERT: A 105 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7957 (tttt) REVERT: A 112 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6800 (p0) REVERT: A 162 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: B 105 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7976 (tttm) REVERT: B 112 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6821 (p0) REVERT: C 282 ASN cc_start: 0.6174 (m110) cc_final: 0.5857 (m110) REVERT: C 355 LYS cc_start: 0.7657 (tptt) cc_final: 0.6947 (tptp) REVERT: C 878 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.5519 (t70) REVERT: C 1010 LYS cc_start: 0.8183 (tptt) cc_final: 0.7819 (ttmt) REVERT: C 1038 GLU cc_start: 0.6528 (mt-10) cc_final: 0.6253 (mt-10) REVERT: F 321 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5787 (mttp) REVERT: F 355 LYS cc_start: 0.7774 (tptt) cc_final: 0.7191 (tptp) REVERT: F 878 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.5542 (t70) REVERT: F 1010 LYS cc_start: 0.8185 (tptt) cc_final: 0.7782 (ttmt) REVERT: F 1038 GLU cc_start: 0.6493 (mt-10) cc_final: 0.6269 (mt-10) outliers start: 50 outliers final: 17 residues processed: 233 average time/residue: 1.2222 time to fit residues: 325.8855 Evaluate side-chains 208 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1062 ASP Chi-restraints excluded: chain F residue 1066 PHE Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 151 GLN A 161 GLN B 151 GLN B 161 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 GLN F 494 ASN F 813 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21136 Z= 0.142 Angle : 0.477 6.859 29302 Z= 0.257 Chirality : 0.035 0.137 3318 Planarity : 0.003 0.034 3048 Dihedral : 16.413 74.372 4982 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.55 % Allowed : 16.35 % Favored : 81.11 % 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: -1.09 (0.18), residues: 1960 helix: 0.91 (0.18), residues: 832 sheet: -0.60 (0.31), residues: 260 loop : -2.48 (0.17), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 38 HIS 0.002 0.001 HIS F 738 PHE 0.013 0.001 PHE F1042 TYR 0.014 0.001 TYR A 26 ARG 0.006 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.948 Fit side-chains REVERT: A 43 ASN cc_start: 0.7417 (m110) cc_final: 0.6989 (m-40) REVERT: A 105 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7875 (tttm) REVERT: A 162 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7346 (pp20) REVERT: B 89 MET cc_start: 0.7923 (ptp) cc_final: 0.7708 (ptm) REVERT: B 105 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7924 (tttm) REVERT: B 162 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7341 (pp20) REVERT: C 282 ASN cc_start: 0.6105 (m110) cc_final: 0.5510 (m110) REVERT: C 355 LYS cc_start: 0.7536 (tptt) cc_final: 0.6781 (tptp) REVERT: C 385 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.7420 (tmm-80) REVERT: C 432 MET cc_start: 0.5947 (tpp) cc_final: 0.5659 (ttp) REVERT: C 878 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5374 (t70) REVERT: C 1010 LYS cc_start: 0.8187 (tptt) cc_final: 0.7716 (ttmt) REVERT: C 1038 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6197 (mt-10) REVERT: F 174 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5811 (p0) REVERT: F 314 MET cc_start: 0.5058 (mmm) cc_final: 0.4483 (mtm) REVERT: F 355 LYS cc_start: 0.7735 (tptt) cc_final: 0.7273 (tptp) REVERT: F 878 ASP cc_start: 0.6408 (OUTLIER) cc_final: 0.5392 (t70) REVERT: F 892 ASN cc_start: 0.6259 (m-40) cc_final: 0.6010 (m-40) REVERT: F 1010 LYS cc_start: 0.8169 (tptt) cc_final: 0.7704 (ttmt) REVERT: F 1038 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6176 (mt-10) REVERT: F 1111 LYS cc_start: 0.7524 (tppt) cc_final: 0.6914 (tttt) outliers start: 45 outliers final: 21 residues processed: 235 average time/residue: 1.2240 time to fit residues: 327.5176 Evaluate side-chains 211 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1062 ASP Chi-restraints excluded: chain F residue 1066 PHE Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 0.6980 chunk 206 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 55 optimal weight: 0.0060 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN C 813 GLN C1112 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21136 Z= 0.176 Angle : 0.494 8.977 29302 Z= 0.264 Chirality : 0.036 0.138 3318 Planarity : 0.003 0.033 3048 Dihedral : 16.339 74.401 4982 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.07 % Allowed : 16.74 % Favored : 79.19 % 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: -0.77 (0.18), residues: 1960 helix: 1.24 (0.19), residues: 832 sheet: -0.43 (0.32), residues: 240 loop : -2.35 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 38 HIS 0.003 0.001 HIS F 738 PHE 0.012 0.001 PHE C 810 TYR 0.016 0.001 TYR B 26 ARG 0.005 0.000 ARG C 921 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 193 time to evaluate : 1.958 Fit side-chains REVERT: A 43 ASN cc_start: 0.7404 (m110) cc_final: 0.6952 (m-40) REVERT: A 105 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7893 (tttm) REVERT: A 162 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7374 (pp20) REVERT: B 43 ASN cc_start: 0.7356 (m110) cc_final: 0.6976 (m-40) REVERT: B 105 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7921 (tttm) REVERT: B 162 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: C 282 ASN cc_start: 0.6093 (m110) cc_final: 0.5626 (m110) REVERT: C 355 LYS cc_start: 0.7536 (tptt) cc_final: 0.6810 (tptp) REVERT: C 408 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7126 (pp20) REVERT: C 432 MET cc_start: 0.6228 (tpp) cc_final: 0.5738 (ttp) REVERT: C 878 ASP cc_start: 0.6336 (OUTLIER) cc_final: 0.5398 (t70) REVERT: C 916 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6599 (tt0) REVERT: C 1010 LYS cc_start: 0.8176 (tptt) cc_final: 0.7809 (ttmt) REVERT: C 1038 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6137 (mt-10) REVERT: F 174 ASP cc_start: 0.6248 (OUTLIER) cc_final: 0.5851 (p0) REVERT: F 355 LYS cc_start: 0.7731 (tptt) cc_final: 0.7256 (tptp) REVERT: F 408 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7218 (pp20) REVERT: F 878 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.5295 (t70) REVERT: F 892 ASN cc_start: 0.6237 (m-40) cc_final: 0.6013 (m-40) REVERT: F 1010 LYS cc_start: 0.8173 (tptt) cc_final: 0.7723 (ttmt) REVERT: F 1038 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6158 (mt-10) outliers start: 72 outliers final: 33 residues processed: 237 average time/residue: 1.1734 time to fit residues: 318.9473 Evaluate side-chains 222 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 916 GLU Chi-restraints excluded: chain C residue 1062 ASP Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1066 PHE Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 161 GLN B 151 GLN B 161 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN C1112 ASN F 178 HIS ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1112 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21136 Z= 0.335 Angle : 0.614 9.975 29302 Z= 0.326 Chirality : 0.041 0.154 3318 Planarity : 0.004 0.040 3048 Dihedral : 16.412 74.320 4982 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.52 % Allowed : 16.57 % Favored : 78.90 % 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: -0.92 (0.18), residues: 1960 helix: 1.01 (0.18), residues: 830 sheet: -0.62 (0.33), residues: 246 loop : -2.28 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP F 424 HIS 0.005 0.001 HIS F 425 PHE 0.017 0.002 PHE C 882 TYR 0.021 0.002 TYR B 26 ARG 0.005 0.001 ARG C 921 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 184 time to evaluate : 2.082 Fit side-chains REVERT: A 105 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7943 (tttp) REVERT: A 113 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7574 (t0) REVERT: A 162 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7507 (pp20) REVERT: B 105 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7948 (tttp) REVERT: B 113 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7572 (t0) REVERT: B 162 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: C 355 LYS cc_start: 0.7662 (tptt) cc_final: 0.7224 (tptp) REVERT: C 408 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: C 432 MET cc_start: 0.6337 (tpp) cc_final: 0.5691 (ttp) REVERT: C 878 ASP cc_start: 0.6378 (OUTLIER) cc_final: 0.5393 (t70) REVERT: C 916 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: C 1010 LYS cc_start: 0.8132 (tptt) cc_final: 0.7749 (ttmt) REVERT: C 1038 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6166 (mt-10) REVERT: F 174 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5854 (p0) REVERT: F 321 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5956 (mttp) REVERT: F 355 LYS cc_start: 0.7771 (tptt) cc_final: 0.7165 (tptp) REVERT: F 408 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7214 (pp20) REVERT: F 878 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.5490 (t70) REVERT: F 1010 LYS cc_start: 0.8132 (tptt) cc_final: 0.7762 (ttmt) REVERT: F 1038 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6174 (mt-10) outliers start: 80 outliers final: 33 residues processed: 236 average time/residue: 1.1461 time to fit residues: 311.4740 Evaluate side-chains 225 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 916 GLU Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 21136 Z= 0.282 Angle : 0.570 7.603 29302 Z= 0.304 Chirality : 0.039 0.147 3318 Planarity : 0.004 0.037 3048 Dihedral : 16.363 74.332 4982 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.86 % Allowed : 17.59 % Favored : 77.55 % 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: -0.82 (0.18), residues: 1960 helix: 1.11 (0.18), residues: 830 sheet: -0.61 (0.33), residues: 246 loop : -2.23 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP F 424 HIS 0.004 0.001 HIS F 738 PHE 0.016 0.002 PHE C 882 TYR 0.020 0.002 TYR A 26 ARG 0.007 0.000 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 182 time to evaluate : 2.091 Fit side-chains REVERT: A 105 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8024 (tttt) REVERT: A 162 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7498 (pp20) REVERT: B 43 ASN cc_start: 0.7540 (m110) cc_final: 0.7192 (m-40) REVERT: B 105 LYS cc_start: 0.8358 (ttmm) cc_final: 0.8021 (tttt) REVERT: B 162 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: C 355 LYS cc_start: 0.7719 (tptt) cc_final: 0.7295 (tptp) REVERT: C 408 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: C 432 MET cc_start: 0.6261 (tpp) cc_final: 0.5666 (ttp) REVERT: C 878 ASP cc_start: 0.6367 (OUTLIER) cc_final: 0.5412 (t70) REVERT: C 919 TYR cc_start: 0.7296 (m-10) cc_final: 0.6824 (m-80) REVERT: C 1010 LYS cc_start: 0.8121 (tptt) cc_final: 0.7740 (ttmt) REVERT: C 1038 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6147 (mt-10) REVERT: F 314 MET cc_start: 0.5948 (OUTLIER) cc_final: 0.4535 (mtp) REVERT: F 355 LYS cc_start: 0.7801 (tptt) cc_final: 0.7181 (tptp) REVERT: F 408 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: F 878 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5390 (t70) REVERT: F 916 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: F 1010 LYS cc_start: 0.8121 (tptt) cc_final: 0.7759 (ttmt) REVERT: F 1038 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6163 (mt-10) outliers start: 86 outliers final: 42 residues processed: 234 average time/residue: 1.1591 time to fit residues: 312.7263 Evaluate side-chains 234 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 184 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 885 VAL Chi-restraints excluded: chain F residue 916 GLU Chi-restraints excluded: chain F residue 974 THR Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 151 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F1112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 21136 Z= 0.151 Angle : 0.480 7.598 29302 Z= 0.257 Chirality : 0.035 0.151 3318 Planarity : 0.003 0.032 3048 Dihedral : 16.181 74.162 4982 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.73 % Allowed : 19.46 % Favored : 76.81 % 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: -0.34 (0.18), residues: 1960 helix: 1.54 (0.18), residues: 838 sheet: 0.02 (0.33), residues: 224 loop : -2.13 (0.17), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 424 HIS 0.003 0.001 HIS C 701 PHE 0.016 0.001 PHE C 810 TYR 0.016 0.001 TYR F 162 ARG 0.007 0.000 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 195 time to evaluate : 1.988 Fit side-chains REVERT: A 43 ASN cc_start: 0.7388 (m110) cc_final: 0.6997 (m-40) REVERT: A 105 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7860 (tttm) REVERT: A 162 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: B 43 ASN cc_start: 0.7321 (m110) cc_final: 0.6936 (m-40) REVERT: B 105 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7866 (tttm) REVERT: B 162 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: C 355 LYS cc_start: 0.7680 (tptt) cc_final: 0.7243 (tptp) REVERT: C 408 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: C 432 MET cc_start: 0.6064 (tpp) cc_final: 0.5741 (ttp) REVERT: C 878 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.5524 (t70) REVERT: C 1010 LYS cc_start: 0.8124 (tptt) cc_final: 0.7763 (ttmt) REVERT: C 1038 GLU cc_start: 0.6385 (mt-10) cc_final: 0.6049 (mt-10) REVERT: F 174 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5837 (p0) REVERT: F 282 ASN cc_start: 0.6030 (OUTLIER) cc_final: 0.5696 (m110) REVERT: F 314 MET cc_start: 0.5734 (OUTLIER) cc_final: 0.4439 (mtm) REVERT: F 355 LYS cc_start: 0.7788 (tptt) cc_final: 0.7169 (tptp) REVERT: F 408 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: F 432 MET cc_start: 0.4667 (ptm) cc_final: 0.4391 (tpp) REVERT: F 878 ASP cc_start: 0.6373 (OUTLIER) cc_final: 0.5421 (t70) REVERT: F 1010 LYS cc_start: 0.8121 (tptt) cc_final: 0.7764 (ttmt) REVERT: F 1038 GLU cc_start: 0.6390 (mt-10) cc_final: 0.6063 (mt-10) outliers start: 66 outliers final: 31 residues processed: 236 average time/residue: 1.2096 time to fit residues: 330.5994 Evaluate side-chains 226 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1112 ASN Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 862 MET Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1112 ASN Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN C1112 ASN F 178 HIS ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21136 Z= 0.232 Angle : 0.534 8.121 29302 Z= 0.285 Chirality : 0.038 0.147 3318 Planarity : 0.003 0.032 3048 Dihedral : 16.181 74.016 4982 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 20.31 % Favored : 76.19 % 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 (0.18), residues: 1960 helix: 1.52 (0.18), residues: 836 sheet: -0.07 (0.34), residues: 226 loop : -2.11 (0.17), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 424 HIS 0.004 0.001 HIS C 178 PHE 0.015 0.002 PHE C 810 TYR 0.017 0.002 TYR B 26 ARG 0.008 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 2.182 Fit side-chains REVERT: A 43 ASN cc_start: 0.7479 (m110) cc_final: 0.7035 (m-40) REVERT: A 105 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7953 (tttt) REVERT: A 162 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7435 (pp20) REVERT: B 43 ASN cc_start: 0.7435 (m110) cc_final: 0.7014 (m-40) REVERT: B 105 LYS cc_start: 0.8295 (ttmm) cc_final: 0.7957 (tttt) REVERT: B 162 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: C 355 LYS cc_start: 0.7724 (tptt) cc_final: 0.7005 (tptp) REVERT: C 408 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7117 (pp20) REVERT: C 432 MET cc_start: 0.6318 (tpp) cc_final: 0.5818 (ttp) REVERT: C 491 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.5940 (ttmt) REVERT: C 878 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.5424 (t70) REVERT: C 919 TYR cc_start: 0.7311 (m-10) cc_final: 0.6831 (m-80) REVERT: C 1010 LYS cc_start: 0.8119 (tptt) cc_final: 0.7745 (ttmt) REVERT: C 1038 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6083 (mt-10) REVERT: F 174 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.6000 (p0) REVERT: F 314 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.4627 (mtp) REVERT: F 321 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5985 (mttp) REVERT: F 355 LYS cc_start: 0.7744 (tptt) cc_final: 0.7146 (tptp) REVERT: F 408 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: F 432 MET cc_start: 0.4732 (ptm) cc_final: 0.4157 (tpp) REVERT: F 491 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6065 (ttmt) REVERT: F 878 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.5414 (t70) REVERT: F 1010 LYS cc_start: 0.8135 (tptt) cc_final: 0.7766 (ttmt) REVERT: F 1038 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6071 (mt-10) outliers start: 62 outliers final: 33 residues processed: 223 average time/residue: 1.1555 time to fit residues: 296.2627 Evaluate side-chains 225 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 693 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 394 HIS Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 491 LYS Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1049 MET Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1112 ASN Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 58 optimal weight: 0.1980 chunk 173 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 813 GLN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21136 Z= 0.246 Angle : 0.551 9.558 29302 Z= 0.293 Chirality : 0.038 0.152 3318 Planarity : 0.004 0.032 3048 Dihedral : 16.197 74.038 4982 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.85 % Allowed : 20.08 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 1960 helix: 1.48 (0.18), residues: 832 sheet: -0.13 (0.34), residues: 226 loop : -2.08 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 424 HIS 0.004 0.001 HIS F 738 PHE 0.018 0.002 PHE C 810 TYR 0.020 0.002 TYR C 923 ARG 0.007 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 182 time to evaluate : 2.167 Fit side-chains REVERT: A 43 ASN cc_start: 0.7504 (m110) cc_final: 0.7127 (m-40) REVERT: A 105 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7964 (tttt) REVERT: A 162 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7462 (pp20) REVERT: B 43 ASN cc_start: 0.7529 (m110) cc_final: 0.7151 (m-40) REVERT: B 105 LYS cc_start: 0.8311 (ttmm) cc_final: 0.7969 (tttt) REVERT: B 162 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: C 146 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6826 (tp) REVERT: C 355 LYS cc_start: 0.7762 (tptt) cc_final: 0.7063 (tptp) REVERT: C 408 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: C 432 MET cc_start: 0.6257 (tpp) cc_final: 0.5702 (ttp) REVERT: C 878 ASP cc_start: 0.6471 (OUTLIER) cc_final: 0.5565 (t70) REVERT: C 919 TYR cc_start: 0.7301 (m-10) cc_final: 0.6888 (m-80) REVERT: C 1010 LYS cc_start: 0.8122 (tptt) cc_final: 0.7740 (ttmt) REVERT: C 1038 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6090 (mt-10) REVERT: F 174 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5919 (p0) REVERT: F 190 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8575 (tmm-80) REVERT: F 314 MET cc_start: 0.5908 (OUTLIER) cc_final: 0.4668 (mtp) REVERT: F 321 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6047 (mttp) REVERT: F 355 LYS cc_start: 0.7766 (tptt) cc_final: 0.7164 (tptp) REVERT: F 408 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7151 (pp20) REVERT: F 432 MET cc_start: 0.4849 (ptm) cc_final: 0.4210 (tpp) REVERT: F 878 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.5435 (t70) REVERT: F 1010 LYS cc_start: 0.8122 (tptt) cc_final: 0.7754 (ttmt) REVERT: F 1038 GLU cc_start: 0.6396 (mt-10) cc_final: 0.6038 (mt-10) outliers start: 68 outliers final: 32 residues processed: 225 average time/residue: 1.1353 time to fit residues: 293.7236 Evaluate side-chains 223 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 321 LYS Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1049 MET Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 213 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 310 ASN ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 HIS C 813 GLN ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN F1112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21136 Z= 0.151 Angle : 0.487 9.549 29302 Z= 0.258 Chirality : 0.035 0.157 3318 Planarity : 0.003 0.032 3048 Dihedral : 16.094 74.044 4982 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.66 % Allowed : 21.32 % Favored : 76.02 % 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: -0.07 (0.19), residues: 1960 helix: 1.77 (0.19), residues: 838 sheet: 0.11 (0.33), residues: 224 loop : -1.97 (0.18), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 424 HIS 0.004 0.001 HIS C 737 PHE 0.020 0.001 PHE C 810 TYR 0.021 0.001 TYR F 307 ARG 0.007 0.000 ARG C 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 1.934 Fit side-chains REVERT: A 43 ASN cc_start: 0.7339 (m110) cc_final: 0.6914 (m-40) REVERT: A 105 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7863 (tttm) REVERT: A 162 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: B 43 ASN cc_start: 0.7324 (m110) cc_final: 0.6937 (m-40) REVERT: B 89 MET cc_start: 0.7845 (ptp) cc_final: 0.7569 (ptm) REVERT: B 105 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7870 (tttm) REVERT: B 162 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7397 (pp20) REVERT: C 355 LYS cc_start: 0.7732 (tptt) cc_final: 0.7016 (tptp) REVERT: C 408 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7016 (pp20) REVERT: C 432 MET cc_start: 0.6290 (tpp) cc_final: 0.5781 (ttp) REVERT: C 878 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.5516 (t70) REVERT: C 919 TYR cc_start: 0.7256 (m-10) cc_final: 0.6806 (m-80) REVERT: C 1010 LYS cc_start: 0.8125 (tptt) cc_final: 0.7744 (ttmt) REVERT: C 1038 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5930 (mt-10) REVERT: F 174 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.6070 (p0) REVERT: F 190 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8522 (tmm-80) REVERT: F 314 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.4686 (mtp) REVERT: F 355 LYS cc_start: 0.7728 (tptt) cc_final: 0.7128 (tptp) REVERT: F 408 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7025 (pp20) REVERT: F 432 MET cc_start: 0.4704 (ptm) cc_final: 0.3994 (tpp) REVERT: F 878 ASP cc_start: 0.6484 (OUTLIER) cc_final: 0.5480 (t70) REVERT: F 1010 LYS cc_start: 0.8098 (tptt) cc_final: 0.7717 (ttmt) REVERT: F 1038 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5907 (mt-10) outliers start: 47 outliers final: 28 residues processed: 211 average time/residue: 1.2136 time to fit residues: 293.8917 Evaluate side-chains 213 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 350 PHE Chi-restraints excluded: chain C residue 394 HIS Chi-restraints excluded: chain C residue 408 GLU Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 737 HIS Chi-restraints excluded: chain C residue 738 HIS Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 1027 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 447 MET Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 693 VAL Chi-restraints excluded: chain F residue 738 HIS Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 856 ASP Chi-restraints excluded: chain F residue 878 ASP Chi-restraints excluded: chain F residue 1027 ASP Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.0020 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 HIS C 813 GLN F 178 HIS ** F 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 813 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.200619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164442 restraints weight = 24038.778| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.57 r_work: 0.3374 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21136 Z= 0.152 Angle : 0.486 10.977 29302 Z= 0.257 Chirality : 0.035 0.152 3318 Planarity : 0.003 0.032 3048 Dihedral : 16.032 74.061 4982 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.88 % Allowed : 21.10 % Favored : 76.02 % 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: 0.06 (0.19), residues: 1960 helix: 1.89 (0.19), residues: 838 sheet: 0.20 (0.33), residues: 224 loop : -1.93 (0.18), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 424 HIS 0.005 0.001 HIS C 737 PHE 0.024 0.001 PHE C 810 TYR 0.019 0.001 TYR C 923 ARG 0.008 0.000 ARG F 921 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.96 seconds wall clock time: 104 minutes 42.21 seconds (6282.21 seconds total)