Starting phenix.real_space_refine on Mon Mar 25 07:17:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghu_40051/03_2024/8ghu_40051_updated.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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 57 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 1531 5.49 5 Mg 83 5.21 5 S 53 5.16 5 C 23726 2.51 5 N 8745 2.21 5 O 13270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "c ARG 71": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "c GLU 160": "OE1" <-> "OE2" Residue "c ARG 178": "NH1" <-> "NH2" Residue "d ARG 183": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "g ARG 94": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 93": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p GLU 45": "OE1" <-> "OE2" 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: 47408 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2260 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain: "a" Number of atoms: 32900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1532, 32900 Unusual residues: {'ZIV': 1} Classifications: {'RNA': 1531, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna2p_pur': 133, 'rna2p_pyr': 110, 'rna3p_pur': 740, 'rna3p_pyr': 548} Link IDs: {'rna2p': 243, 'rna3p': 1286, None: 2} Not linked: pdbres=" C a1404 " pdbres="ZIV a1405 " Not linked: pdbres="ZIV a1405 " pdbres=" U a1406 " Chain: "c" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "a" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Unusual residues: {' MG': 79} Classifications: {'undetermined': 79} Link IDs: {None: 78} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 470 residue: pdb=" P C a 930 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 930 " occ=0.00 residue: pdb=" P C a 931 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 931 " occ=0.00 residue: pdb=" P C a 932 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 932 " occ=0.00 residue: pdb=" P G a 933 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 933 " occ=0.00 residue: pdb=" P C a 934 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 934 " occ=0.00 residue: pdb=" P A a 935 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 935 " occ=0.00 residue: pdb=" P C a 936 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 936 " occ=0.00 residue: pdb=" P A a 937 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 937 " occ=0.00 residue: pdb=" P A a 938 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 938 " occ=0.00 residue: pdb=" P G a 939 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 939 " occ=0.00 residue: pdb=" P C a 940 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 940 " occ=0.00 residue: pdb=" P G a 941 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 941 " occ=0.00 ... (remaining 458 not shown) Time building chain proxies: 24.38, per 1000 atoms: 0.51 Number of scatterers: 47408 At special positions: 0 Unit cell: (185.229, 240.318, 156.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 1531 15.00 Mg 83 11.99 O 13270 8.00 N 8745 7.00 C 23726 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 18 sheets defined 26.0% alpha, 8.2% beta 140 base pairs and 754 stacking pairs defined. Time for finding SS restraints: 21.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 9 through 17 removed outlier: 4.241A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.565A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 66 through 72 removed outlier: 4.662A pdb=" N LYS A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 89 through 102 removed outlier: 3.608A pdb=" N TRP A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 144 through 150 removed outlier: 3.920A pdb=" N ALA A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.965A pdb=" N ALA A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.350A pdb=" N GLN A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.652A pdb=" N LYS A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 254' Processing helix chain 'c' and resid 33 through 35 No H-bonds generated for 'chain 'c' and resid 33 through 35' Processing helix chain 'c' and resid 37 through 43 removed outlier: 4.393A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 94 removed outlier: 3.641A pdb=" N ARG c 87 " --> pdb=" O VAL c 83 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL c 90 " --> pdb=" O LEU c 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA c 94 " --> pdb=" O VAL c 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 83 through 94' Processing helix chain 'c' and resid 114 through 125 removed outlier: 3.735A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 141 removed outlier: 3.777A pdb=" N MET c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN c 138 " --> pdb=" O LYS c 134 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 removed outlier: 3.815A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 7 through 12' Processing helix chain 'd' and resid 49 through 64 removed outlier: 3.644A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG d 55 " --> pdb=" O GLY d 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS d 57 " --> pdb=" O GLN d 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 78 removed outlier: 4.030A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 94 removed outlier: 4.029A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA d 91 " --> pdb=" O GLU d 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU d 92 " --> pdb=" O ASN d 88 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 100 No H-bonds generated for 'chain 'd' and resid 97 through 100' Processing helix chain 'd' and resid 102 through 104 No H-bonds generated for 'chain 'd' and resid 102 through 104' Processing helix chain 'd' and resid 110 through 116 removed outlier: 3.546A pdb=" N ARG d 114 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 158 removed outlier: 3.804A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU d 158 " --> pdb=" O VAL d 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 152 through 158' Processing helix chain 'e' and resid 55 through 67 removed outlier: 3.504A pdb=" N ALA e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET e 63 " --> pdb=" O ILE e 59 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 117 removed outlier: 3.685A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 135 No H-bonds generated for 'chain 'e' and resid 132 through 135' Processing helix chain 'e' and resid 139 through 143 Processing helix chain 'e' and resid 149 through 153 Processing helix chain 'f' and resid 18 through 21 No H-bonds generated for 'chain 'f' and resid 18 through 21' Processing helix chain 'f' and resid 68 through 74 removed outlier: 3.883A pdb=" N ASP f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 80 No H-bonds generated for 'chain 'f' and resid 77 through 80' Processing helix chain 'g' and resid 59 through 66 removed outlier: 3.859A pdb=" N VAL g 63 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA g 64 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU g 66 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 101 through 106 removed outlier: 3.545A pdb=" N GLU g 105 " --> pdb=" O ARG g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 120 removed outlier: 3.836A pdb=" N LEU g 119 " --> pdb=" O MET g 115 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA g 120 " --> pdb=" O ALA g 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 115 through 120' Processing helix chain 'g' and resid 138 through 143 Processing helix chain 'h' and resid 5 through 19 removed outlier: 3.645A pdb=" N MET h 9 " --> pdb=" O PRO h 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE h 13 " --> pdb=" O MET h 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN h 17 " --> pdb=" O ILE h 13 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA h 19 " --> pdb=" O ASN h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 41 removed outlier: 3.802A pdb=" N ALA h 34 " --> pdb=" O LYS h 30 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU h 41 " --> pdb=" O ASN h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 90 No H-bonds generated for 'chain 'h' and resid 88 through 90' Processing helix chain 'h' and resid 94 through 97 Processing helix chain 'l' and resid 3 through 5 No H-bonds generated for 'chain 'l' and resid 3 through 5' Processing helix chain 'm' and resid 45 through 47 No H-bonds generated for 'chain 'm' and resid 45 through 47' Processing helix chain 'm' and resid 50 through 57 removed outlier: 3.597A pdb=" N ILE m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP m 54 " --> pdb=" O GLY m 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR m 55 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG m 57 " --> pdb=" O ASP m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 69 through 72 No H-bonds generated for 'chain 'm' and resid 69 through 72' Processing helix chain 'm' and resid 87 through 91 Processing helix chain 'o' and resid 9 through 14 removed outlier: 4.267A pdb=" N SER o 13 " --> pdb=" O ALA o 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU o 14 " --> pdb=" O LYS o 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 9 through 14' Processing helix chain 'o' and resid 27 through 43 removed outlier: 4.123A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU o 39 " --> pdb=" O GLN o 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE o 43 " --> pdb=" O LEU o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 67 removed outlier: 3.905A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU o 57 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG o 58 " --> pdb=" O ARG o 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER o 61 " --> pdb=" O LEU o 57 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN o 62 " --> pdb=" O ARG o 58 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG o 63 " --> pdb=" O MET o 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG o 64 " --> pdb=" O VAL o 60 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS o 65 " --> pdb=" O SER o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 84 removed outlier: 3.718A pdb=" N GLN o 80 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU o 81 " --> pdb=" O TYR o 78 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE o 82 " --> pdb=" O THR o 79 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU o 83 " --> pdb=" O GLN o 80 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG o 84 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 57 No H-bonds generated for 'chain 'p' and resid 54 through 57' Processing helix chain 'p' and resid 69 through 76 removed outlier: 3.588A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU p 74 " --> pdb=" O ARG p 70 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE p 75 " --> pdb=" O VAL p 71 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 69 through 76' Processing helix chain 'r' and resid 28 through 30 No H-bonds generated for 'chain 'r' and resid 28 through 30' Processing helix chain 'r' and resid 59 through 62 Processing helix chain 't' and resid 4 through 24 removed outlier: 3.990A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA t 21 " --> pdb=" O ARG t 17 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG t 23 " --> pdb=" O HIS t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 26 through 40 removed outlier: 4.070A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS t 33 " --> pdb=" O THR t 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR t 35 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA t 36 " --> pdb=" O LYS t 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE t 38 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 48 No H-bonds generated for 'chain 't' and resid 45 through 48' Processing helix chain 't' and resid 50 through 57 removed outlier: 3.627A pdb=" N GLN t 54 " --> pdb=" O PHE t 50 " (cutoff:3.500A) Proline residue: t 55 - end of helix No H-bonds generated for 'chain 't' and resid 50 through 57' Processing helix chain 't' and resid 70 through 77 removed outlier: 3.577A pdb=" N ALA t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) Processing helix chain 't' and resid 79 through 85 removed outlier: 3.537A pdb=" N ASN t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.097A pdb=" N LEU A 199 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA A 135 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 201 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 262 through 267 removed outlier: 7.019A pdb=" N ILE A 277 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'c' and resid 54 through 56 removed outlier: 3.782A pdb=" N VAL c 55 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'c' and resid 148 through 151 removed outlier: 4.915A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP c 182 " --> pdb=" O ILE c 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'd' and resid 122 through 124 removed outlier: 3.980A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE d 181 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'e' and resid 18 through 21 Processing sheet with id= G, first strand: chain 'e' and resid 35 through 38 removed outlier: 3.723A pdb=" N VAL e 38 " --> pdb=" O GLY e 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY e 46 " --> pdb=" O VAL e 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.532A pdb=" N VAL e 84 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'f' and resid 6 through 8 Processing sheet with id= J, first strand: chain 'f' and resid 36 through 41 removed outlier: 6.588A pdb=" N ASN f 63 " --> pdb=" O HIS f 37 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU f 39 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU f 61 " --> pdb=" O LEU f 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'h' and resid 23 through 27 removed outlier: 3.946A pdb=" N LEU h 60 " --> pdb=" O VAL h 24 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU h 59 " --> pdb=" O LYS h 49 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS h 49 " --> pdb=" O GLU h 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'h' and resid 100 through 105 removed outlier: 3.800A pdb=" N VAL h 102 " --> pdb=" O CYS h 126 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS h 126 " --> pdb=" O VAL h 102 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER h 104 " --> pdb=" O ILE h 124 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE h 124 " --> pdb=" O SER h 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'l' and resid 29 through 32 removed outlier: 3.651A pdb=" N ARG l 82 " --> pdb=" O HIS l 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS l 95 " --> pdb=" O ARG l 82 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'l' and resid 53 through 55 removed outlier: 3.607A pdb=" N VAL l 54 " --> pdb=" O VAL l 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL l 62 " --> pdb=" O VAL l 54 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'p' and resid 2 through 8 removed outlier: 3.700A pdb=" N ALA p 22 " --> pdb=" O THR p 3 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG p 5 " --> pdb=" O VAL p 20 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL p 20 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL p 21 " --> pdb=" O ARG p 35 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ARG p 35 " --> pdb=" O VAL p 21 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'q' and resid 9 through 12 removed outlier: 3.583A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU q 43 " --> pdb=" O VAL q 22 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'q' and resid 25 through 29 removed outlier: 3.952A pdb=" N VAL q 28 " --> pdb=" O ILE q 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE q 37 " --> pdb=" O VAL q 28 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'q' and resid 60 through 62 removed outlier: 4.192A pdb=" N ARG q 61 " --> pdb=" O THR q 73 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR q 73 " --> pdb=" O ARG q 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 151 hydrogen bonds defined for protein. 414 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 754 stacking parallelities Total time for adding SS restraints: 36.25 Time building geometry restraints manager: 23.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3842 1.29 - 1.42: 22420 1.42 - 1.55: 22049 1.55 - 1.68: 3064 1.68 - 1.81: 95 Bond restraints: 51470 Sorted by residual: bond pdb=" C43 ZIV a1405 " pdb=" C45 ZIV a1405 " ideal model delta sigma weight residual 1.280 1.533 -0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C35 ZIV a1405 " pdb=" C45 ZIV a1405 " ideal model delta sigma weight residual 1.570 1.372 0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" C35 ZIV a1405 " pdb=" N34 ZIV a1405 " ideal model delta sigma weight residual 1.326 1.470 -0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" C21 ZIV a1405 " pdb=" N22 ZIV a1405 " ideal model delta sigma weight residual 1.324 1.436 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C19 ZIV a1405 " pdb=" O20 ZIV a1405 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.63e+01 ... (remaining 51465 not shown) Histogram of bond angle deviations from ideal: 93.30 - 101.67: 1525 101.67 - 110.04: 23162 110.04 - 118.41: 25161 118.41 - 126.78: 22967 126.78 - 135.15: 4305 Bond angle restraints: 77120 Sorted by residual: angle pdb=" N TYR A 60 " pdb=" CA TYR A 60 " pdb=" C TYR A 60 " ideal model delta sigma weight residual 113.23 101.44 11.79 1.24e+00 6.50e-01 9.04e+01 angle pdb=" O3' G a1530 " pdb=" C3' G a1530 " pdb=" C2' G a1530 " ideal model delta sigma weight residual 109.50 121.19 -11.69 1.50e+00 4.44e-01 6.08e+01 angle pdb=" N PRO A 41 " pdb=" CA PRO A 41 " pdb=" C PRO A 41 " ideal model delta sigma weight residual 110.70 119.85 -9.15 1.22e+00 6.72e-01 5.63e+01 angle pdb=" N34 ZIV a1405 " pdb=" C35 ZIV a1405 " pdb=" O36 ZIV a1405 " ideal model delta sigma weight residual 110.19 132.55 -22.36 3.00e+00 1.11e-01 5.56e+01 angle pdb=" O3' C a1210 " pdb=" C3' C a1210 " pdb=" C2' C a1210 " ideal model delta sigma weight residual 109.50 120.42 -10.92 1.50e+00 4.44e-01 5.30e+01 ... (remaining 77115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 29246 35.97 - 71.94: 3341 71.94 - 107.91: 405 107.91 - 143.88: 6 143.88 - 179.84: 17 Dihedral angle restraints: 33015 sinusoidal: 27753 harmonic: 5262 Sorted by residual: dihedral pdb=" C4' C a1038 " pdb=" C3' C a1038 " pdb=" C2' C a1038 " pdb=" C1' C a1038 " ideal model delta sinusoidal sigma weight residual -35.00 31.77 -66.77 1 8.00e+00 1.56e-02 9.08e+01 dihedral pdb=" C5' C a1038 " pdb=" C4' C a1038 " pdb=" C3' C a1038 " pdb=" O3' C a1038 " ideal model delta sinusoidal sigma weight residual 147.00 81.93 65.07 1 8.00e+00 1.56e-02 8.68e+01 dihedral pdb=" O4' C a1192 " pdb=" C1' C a1192 " pdb=" N1 C a1192 " pdb=" C2 C a1192 " ideal model delta sinusoidal sigma weight residual 200.00 53.81 146.19 1 1.50e+01 4.44e-03 7.81e+01 ... (remaining 33012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 9447 0.143 - 0.285: 365 0.285 - 0.428: 55 0.428 - 0.571: 4 0.571 - 0.713: 2 Chirality restraints: 9873 Sorted by residual: chirality pdb=" C3' C a1210 " pdb=" C4' C a1210 " pdb=" O3' C a1210 " pdb=" C2' C a1210 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C3' U a1049 " pdb=" C4' U a1049 " pdb=" O3' U a1049 " pdb=" C2' U a1049 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" C3' G a1530 " pdb=" C4' G a1530 " pdb=" O3' G a1530 " pdb=" C2' G a1530 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 9870 not shown) Planarity restraints: 4069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 98 " 0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C ALA e 98 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA e 98 " 0.032 2.00e-02 2.50e+03 pdb=" N SER e 99 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 230 " -0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL A 230 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL A 230 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 231 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 ZIV a1405 " -0.009 2.00e-02 2.50e+03 1.85e-02 1.12e+01 pdb=" C03 ZIV a1405 " 0.001 2.00e-02 2.50e+03 pdb=" C05 ZIV a1405 " 0.033 2.00e-02 2.50e+03 pdb=" C33 ZIV a1405 " -0.004 2.00e-02 2.50e+03 pdb=" C35 ZIV a1405 " -0.027 2.00e-02 2.50e+03 pdb=" C47 ZIV a1405 " 0.011 2.00e-02 2.50e+03 pdb=" C49 ZIV a1405 " -0.003 2.00e-02 2.50e+03 pdb=" N04 ZIV a1405 " -0.012 2.00e-02 2.50e+03 pdb=" N34 ZIV a1405 " -0.001 2.00e-02 2.50e+03 pdb=" N48 ZIV a1405 " 0.040 2.00e-02 2.50e+03 pdb=" N50 ZIV a1405 " -0.000 2.00e-02 2.50e+03 pdb=" N51 ZIV a1405 " -0.007 2.00e-02 2.50e+03 pdb=" O01 ZIV a1405 " -0.024 2.00e-02 2.50e+03 ... (remaining 4066 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4707 2.73 - 3.27: 39195 3.27 - 3.82: 84516 3.82 - 4.36: 109744 4.36 - 4.90: 147423 Nonbonded interactions: 385585 Sorted by model distance: nonbonded pdb=" O18 ZIV a1405 " pdb=" O20 ZIV a1405 " model vdw 2.190 2.432 nonbonded pdb=" N1 G a 413 " pdb=" CE LYS d 32 " model vdw 2.200 3.520 nonbonded pdb=" O LEU A 257 " pdb=" CD2 LEU A 257 " model vdw 2.235 3.460 nonbonded pdb=" O2' A a 563 " pdb=" O2' G a 566 " model vdw 2.254 2.440 nonbonded pdb=" O4 U a 652 " pdb=" O2' G a 752 " model vdw 2.264 2.440 ... (remaining 385580 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.79 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.050 Extract box with map and model: 15.500 Check model and map are aligned: 0.750 Set scattering table: 0.470 Process input model: 145.170 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.253 51470 Z= 0.347 Angle : 0.738 22.360 77120 Z= 0.482 Chirality : 0.055 0.713 9873 Planarity : 0.003 0.050 4069 Dihedral : 22.440 179.845 29619 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.06 % Favored : 88.89 % Rotamer: Outliers : 3.01 % Allowed : 9.24 % Favored : 87.75 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.15), residues: 1800 helix: -4.66 (0.11), residues: 379 sheet: -2.31 (0.37), residues: 176 loop : -2.91 (0.14), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 224 HIS 0.006 0.001 HIS A 105 PHE 0.016 0.001 PHE A 37 TYR 0.016 0.001 TYR A 275 ARG 0.004 0.000 ARG g 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 448 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5928 (mmm) cc_final: 0.5505 (mmm) REVERT: A 49 VAL cc_start: 0.3873 (p) cc_final: 0.3579 (t) REVERT: A 57 TYR cc_start: 0.5633 (t80) cc_final: 0.5298 (t80) REVERT: A 124 GLU cc_start: 0.4024 (OUTLIER) cc_final: 0.3202 (pm20) REVERT: A 188 ASP cc_start: 0.4955 (OUTLIER) cc_final: 0.4286 (t0) REVERT: A 206 TYR cc_start: -0.2419 (m-80) cc_final: -0.2891 (m-10) REVERT: A 246 GLU cc_start: -0.0320 (OUTLIER) cc_final: -0.1842 (tm-30) REVERT: c 54 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6037 (pp) REVERT: c 104 GLU cc_start: 0.4286 (mp0) cc_final: 0.3796 (tp30) REVERT: c 120 THR cc_start: 0.5671 (m) cc_final: 0.4854 (t) REVERT: d 123 MET cc_start: 0.7500 (mtt) cc_final: 0.7255 (mtp) REVERT: d 150 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6809 (pptt) REVERT: d 182 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.5646 (tmtt) REVERT: e 60 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8163 (tm-30) REVERT: f 4 TYR cc_start: 0.6648 (m-80) cc_final: 0.6204 (m-80) REVERT: f 42 TRP cc_start: 0.5375 (m100) cc_final: 0.4783 (m100) REVERT: f 88 MET cc_start: 0.6983 (tpp) cc_final: 0.6321 (mtt) REVERT: g 110 ARG cc_start: 0.2715 (tpt170) cc_final: 0.2456 (ptm160) REVERT: g 115 MET cc_start: -0.2632 (ptm) cc_final: -0.3075 (pmm) REVERT: h 33 VAL cc_start: 0.8425 (t) cc_final: 0.8043 (t) REVERT: m 31 LYS cc_start: 0.4603 (pttp) cc_final: 0.4131 (tppt) REVERT: o 26 GLU cc_start: 0.5115 (mt-10) cc_final: 0.4899 (mp0) REVERT: o 51 HIS cc_start: 0.7657 (t70) cc_final: 0.7407 (m90) REVERT: o 79 THR cc_start: 0.8178 (p) cc_final: 0.7710 (p) outliers start: 46 outliers final: 5 residues processed: 480 average time/residue: 1.8502 time to fit residues: 1068.4744 Evaluate side-chains 223 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain q residue 48 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 193 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN c 40 GLN ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 189 HIS d 35 GLN d 39 GLN d 53 GLN d 58 GLN d 70 GLN d 115 GLN d 163 GLN e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 ASN h 37 ASN l 4 ASN m 91 HIS o 51 HIS ** o 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 GLN r 73 HIS t 2 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 51470 Z= 0.526 Angle : 0.871 12.670 77120 Z= 0.428 Chirality : 0.043 0.387 9873 Planarity : 0.007 0.085 4069 Dihedral : 23.551 179.181 26004 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.61 % Favored : 93.33 % Rotamer: Outliers : 7.99 % Allowed : 19.72 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.16), residues: 1800 helix: -3.86 (0.15), residues: 489 sheet: -1.85 (0.33), residues: 218 loop : -2.78 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP c 200 HIS 0.010 0.003 HIS o 50 PHE 0.029 0.004 PHE A 144 TYR 0.037 0.004 TYR r 69 ARG 0.039 0.001 ARG d 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 290 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6566 (mmm) cc_final: 0.6157 (mmm) REVERT: A 16 LEU cc_start: 0.6052 (pp) cc_final: 0.5503 (tp) REVERT: c 45 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5430 (pp20) REVERT: c 129 PHE cc_start: 0.5753 (OUTLIER) cc_final: 0.4756 (p90) REVERT: c 148 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7240 (mp) REVERT: c 182 ASP cc_start: 0.7803 (p0) cc_final: 0.7469 (p0) REVERT: c 190 THR cc_start: -0.0883 (p) cc_final: -0.1192 (m) REVERT: d 150 LYS cc_start: 0.7707 (mmtt) cc_final: 0.6824 (pttm) REVERT: e 31 SER cc_start: 0.8984 (m) cc_final: 0.8593 (t) REVERT: e 33 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9180 (t) REVERT: e 60 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8176 (tm-30) REVERT: f 2 ARG cc_start: 0.7238 (mpp80) cc_final: 0.6804 (mtt180) REVERT: f 42 TRP cc_start: 0.6429 (m100) cc_final: 0.5729 (m100) REVERT: f 49 TYR cc_start: 0.3579 (OUTLIER) cc_final: 0.2090 (p90) REVERT: g 9 ARG cc_start: 0.1856 (mtt180) cc_final: 0.0869 (ttt-90) REVERT: g 100 MET cc_start: 0.1745 (OUTLIER) cc_final: 0.1198 (mpt) REVERT: g 108 ARG cc_start: 0.3082 (OUTLIER) cc_final: 0.1103 (mtt180) REVERT: g 115 MET cc_start: -0.2694 (ptm) cc_final: -0.3037 (pmm) REVERT: g 122 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.4118 (mt-10) REVERT: g 143 MET cc_start: 0.1603 (ppp) cc_final: -0.0731 (tpp) REVERT: h 55 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7043 (mppt) REVERT: l 43 LYS cc_start: 0.8001 (mttt) cc_final: 0.7678 (tppt) REVERT: p 51 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7584 (ptp-110) REVERT: q 10 ARG cc_start: 0.7886 (tpp-160) cc_final: 0.7529 (tpp-160) REVERT: q 13 SER cc_start: 0.8842 (m) cc_final: 0.8067 (t) outliers start: 122 outliers final: 41 residues processed: 379 average time/residue: 1.6855 time to fit residues: 785.0338 Evaluate side-chains 248 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 49 TYR Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain g residue 122 GLU Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 55 LYS Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 81 ILE Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 67 HIS Chi-restraints excluded: chain t residue 85 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 325 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN c 40 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 ASN d 139 ASN e 18 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN f 46 GLN f 68 GLN h 3 GLN h 37 ASN ** o 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 51470 Z= 0.205 Angle : 0.546 9.028 77120 Z= 0.279 Chirality : 0.032 0.343 9873 Planarity : 0.005 0.064 4069 Dihedral : 23.401 179.370 25984 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 7.08 % Allowed : 24.90 % Favored : 68.02 % 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: -3.83 (0.17), residues: 1800 helix: -3.27 (0.17), residues: 503 sheet: -1.62 (0.33), residues: 227 loop : -2.46 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 93 HIS 0.005 0.001 HIS o 42 PHE 0.018 0.002 PHE p 32 TYR 0.014 0.002 TYR r 69 ARG 0.015 0.001 ARG e 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 230 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6623 (mmm) cc_final: 0.6185 (mmm) REVERT: A 16 LEU cc_start: 0.6272 (pp) cc_final: 0.5824 (tp) REVERT: A 152 MET cc_start: 0.3525 (ppp) cc_final: 0.3134 (pmm) REVERT: A 180 GLU cc_start: 0.4584 (tm-30) cc_final: 0.3990 (mp0) REVERT: c 126 ARG cc_start: 0.3873 (mtt90) cc_final: 0.3473 (mpp-170) REVERT: c 182 ASP cc_start: 0.7817 (p0) cc_final: 0.7450 (p0) REVERT: c 190 THR cc_start: -0.0907 (p) cc_final: -0.1237 (m) REVERT: e 60 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8138 (tm-30) REVERT: e 71 ILE cc_start: 0.8673 (tt) cc_final: 0.8401 (pp) REVERT: g 9 ARG cc_start: 0.1830 (mtt180) cc_final: 0.0762 (ttt-90) REVERT: g 100 MET cc_start: 0.1611 (OUTLIER) cc_final: 0.1318 (mpt) REVERT: g 110 ARG cc_start: 0.3079 (tpt170) cc_final: 0.2875 (ptm160) REVERT: g 115 MET cc_start: -0.2386 (ptm) cc_final: -0.2604 (pmm) REVERT: g 122 GLU cc_start: 0.4453 (mt-10) cc_final: 0.4179 (mt-10) REVERT: g 143 MET cc_start: 0.1202 (ppp) cc_final: -0.0755 (mtt) REVERT: h 49 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8622 (ptpp) REVERT: l 43 LYS cc_start: 0.8027 (mttt) cc_final: 0.7667 (tppt) REVERT: l 79 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8539 (tt) REVERT: o 26 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6547 (mp0) REVERT: p 51 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7818 (ptp-170) REVERT: q 13 SER cc_start: 0.8609 (m) cc_final: 0.7891 (t) REVERT: q 62 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: t 53 MET cc_start: 0.8539 (tmm) cc_final: 0.8330 (tmm) outliers start: 108 outliers final: 42 residues processed: 299 average time/residue: 1.5599 time to fit residues: 578.5927 Evaluate side-chains 244 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 197 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 125 ARG Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 49 LYS Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 104 SER Chi-restraints excluded: chain o residue 8 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 156 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 319 optimal weight: 1.9990 chunk 157 optimal weight: 40.0000 chunk 286 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN c 184 ASN d 151 GLN e 72 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 3 GLN ** o 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 HIS r 73 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 51470 Z= 0.252 Angle : 0.589 8.848 77120 Z= 0.300 Chirality : 0.033 0.310 9873 Planarity : 0.005 0.054 4069 Dihedral : 23.529 179.276 25984 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 7.47 % Allowed : 24.77 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.52 (0.18), residues: 1800 helix: -2.77 (0.18), residues: 531 sheet: -1.18 (0.34), residues: 221 loop : -2.43 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 200 HIS 0.008 0.001 HIS f 37 PHE 0.019 0.002 PHE f 8 TYR 0.027 0.002 TYR A 275 ARG 0.007 0.001 ARG d 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 226 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6343 (mmm) cc_final: 0.5946 (mmm) REVERT: A 16 LEU cc_start: 0.6448 (pp) cc_final: 0.6178 (tp) REVERT: A 152 MET cc_start: 0.3203 (ppp) cc_final: 0.2873 (ppp) REVERT: A 219 LYS cc_start: 0.4182 (ptpt) cc_final: 0.3380 (pptt) REVERT: A 257 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2236 (tm) REVERT: c 17 TRP cc_start: 0.5577 (m100) cc_final: 0.4691 (m-90) REVERT: c 41 TYR cc_start: 0.7514 (t80) cc_final: 0.7229 (t80) REVERT: c 45 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5727 (pp20) REVERT: c 129 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4398 (p90) REVERT: c 182 ASP cc_start: 0.7507 (p0) cc_final: 0.7209 (p0) REVERT: d 17 ASP cc_start: 0.8576 (t0) cc_final: 0.8375 (t0) REVERT: d 62 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7921 (mpt-90) REVERT: d 115 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7356 (tp40) REVERT: d 194 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7317 (pt) REVERT: e 31 SER cc_start: 0.8960 (m) cc_final: 0.8534 (t) REVERT: e 60 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7990 (tm-30) REVERT: f 21 MET cc_start: 0.7557 (mtp) cc_final: 0.7314 (mtm) REVERT: f 65 GLU cc_start: 0.7952 (mp0) cc_final: 0.7501 (mp0) REVERT: g 9 ARG cc_start: 0.1908 (mtt180) cc_final: 0.0803 (ttt-90) REVERT: g 100 MET cc_start: 0.1838 (OUTLIER) cc_final: 0.1463 (mpt) REVERT: g 108 ARG cc_start: 0.2654 (OUTLIER) cc_final: 0.0870 (mtp180) REVERT: g 110 ARG cc_start: 0.3178 (tpt170) cc_final: 0.2691 (mtp-110) REVERT: g 122 GLU cc_start: 0.4444 (mt-10) cc_final: 0.4068 (mt-10) REVERT: g 143 MET cc_start: 0.1436 (ppp) cc_final: -0.0446 (mtt) REVERT: h 49 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8535 (pmmt) REVERT: l 43 LYS cc_start: 0.8245 (mttt) cc_final: 0.7858 (tppt) REVERT: l 55 ARG cc_start: 0.7989 (tmm-80) cc_final: 0.7726 (ttp-110) REVERT: l 76 HIS cc_start: 0.8320 (m-70) cc_final: 0.7938 (m-70) REVERT: o 5 THR cc_start: 0.8093 (t) cc_final: 0.7864 (p) REVERT: p 51 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7735 (ptp-170) REVERT: q 13 SER cc_start: 0.8744 (m) cc_final: 0.8071 (t) REVERT: q 80 LYS cc_start: 0.8702 (tttt) cc_final: 0.8269 (tptm) REVERT: t 53 MET cc_start: 0.8570 (tmm) cc_final: 0.8316 (tmm) outliers start: 114 outliers final: 44 residues processed: 307 average time/residue: 1.6306 time to fit residues: 619.9259 Evaluate side-chains 246 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 192 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 62 ARG Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 15 ILE Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 22 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 49 LYS Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 8 GLN Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 0.7980 chunk 181 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 132 optimal weight: 50.0000 chunk 273 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 287 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 130 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN f 68 GLN o 42 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.7383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 51470 Z= 0.123 Angle : 0.474 10.252 77120 Z= 0.242 Chirality : 0.029 0.250 9873 Planarity : 0.004 0.044 4069 Dihedral : 23.390 179.946 25984 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.85 % Allowed : 28.90 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.08 (0.18), residues: 1800 helix: -2.23 (0.20), residues: 538 sheet: -0.95 (0.33), residues: 241 loop : -2.26 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 200 HIS 0.023 0.001 HIS t 67 PHE 0.011 0.001 PHE A 146 TYR 0.015 0.001 TYR A 275 ARG 0.007 0.001 ARG e 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 195 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6331 (mmm) cc_final: 0.5967 (mmm) REVERT: A 16 LEU cc_start: 0.6305 (pp) cc_final: 0.6092 (tp) REVERT: A 111 ARG cc_start: 0.1798 (OUTLIER) cc_final: 0.1386 (ttm170) REVERT: A 152 MET cc_start: 0.3573 (ppp) cc_final: 0.3252 (ppp) REVERT: c 17 TRP cc_start: 0.5491 (m100) cc_final: 0.4582 (m-90) REVERT: c 129 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4322 (p90) REVERT: c 182 ASP cc_start: 0.7411 (p0) cc_final: 0.7062 (p0) REVERT: e 31 SER cc_start: 0.8946 (m) cc_final: 0.8551 (t) REVERT: f 21 MET cc_start: 0.7303 (mtp) cc_final: 0.7033 (mtp) REVERT: f 91 ARG cc_start: 0.7622 (tpt-90) cc_final: 0.7021 (tpt-90) REVERT: g 9 ARG cc_start: 0.1927 (mtt180) cc_final: 0.0751 (ttt-90) REVERT: g 110 ARG cc_start: 0.3157 (tpt170) cc_final: 0.2691 (mtp-110) REVERT: g 143 MET cc_start: 0.1085 (ppp) cc_final: -0.0557 (mtt) REVERT: l 43 LYS cc_start: 0.8223 (mttt) cc_final: 0.7792 (tppt) REVERT: o 5 THR cc_start: 0.8048 (t) cc_final: 0.7826 (p) REVERT: o 63 ARG cc_start: 0.7616 (mmp80) cc_final: 0.6139 (mmt90) REVERT: q 13 SER cc_start: 0.8620 (m) cc_final: 0.7978 (t) REVERT: q 62 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: q 80 LYS cc_start: 0.8756 (tttt) cc_final: 0.8309 (tptm) outliers start: 74 outliers final: 32 residues processed: 248 average time/residue: 1.5883 time to fit residues: 492.8883 Evaluate side-chains 213 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 62 GLU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain t residue 3 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 320 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 148 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 168 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN f 58 HIS f 68 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.8300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 51470 Z= 0.354 Angle : 0.642 11.171 77120 Z= 0.322 Chirality : 0.035 0.241 9873 Planarity : 0.005 0.050 4069 Dihedral : 23.712 179.757 25981 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.72 % Favored : 92.22 % Rotamer: Outliers : 6.36 % Allowed : 27.46 % Favored : 66.19 % 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: -3.15 (0.18), residues: 1800 helix: -2.30 (0.20), residues: 543 sheet: -0.95 (0.32), residues: 252 loop : -2.32 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 200 HIS 0.010 0.002 HIS t 67 PHE 0.020 0.002 PHE f 8 TYR 0.036 0.003 TYR A 275 ARG 0.012 0.001 ARG d 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 195 time to evaluate : 3.062 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6007 (mmm) cc_final: 0.5661 (mmm) REVERT: A 111 ARG cc_start: 0.2221 (OUTLIER) cc_final: 0.1206 (tpp-160) REVERT: A 219 LYS cc_start: 0.3963 (ptpt) cc_final: 0.3202 (pptt) REVERT: A 257 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2396 (tm) REVERT: c 17 TRP cc_start: 0.5721 (m100) cc_final: 0.4842 (m-90) REVERT: c 45 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5957 (pp20) REVERT: c 129 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.4317 (p90) REVERT: c 182 ASP cc_start: 0.7630 (p0) cc_final: 0.7100 (p0) REVERT: d 17 ASP cc_start: 0.8561 (t0) cc_final: 0.8359 (t0) REVERT: d 115 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7347 (tp40) REVERT: e 31 SER cc_start: 0.8945 (m) cc_final: 0.8567 (t) REVERT: e 115 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7970 (pp20) REVERT: e 151 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7145 (ptp) REVERT: g 110 ARG cc_start: 0.3462 (tpt170) cc_final: 0.2977 (mtp-110) REVERT: g 143 MET cc_start: 0.1433 (ppp) cc_final: -0.0298 (mtt) REVERT: h 59 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7477 (mm-30) REVERT: l 43 LYS cc_start: 0.8351 (mttt) cc_final: 0.8002 (tppt) REVERT: m 75 MET cc_start: 0.3969 (tmm) cc_final: 0.3563 (tmm) REVERT: o 53 ARG cc_start: 0.7877 (mtp-110) cc_final: 0.6768 (mmp-170) REVERT: o 62 GLN cc_start: 0.7100 (mt0) cc_final: 0.6789 (mt0) REVERT: o 63 ARG cc_start: 0.7631 (mmp80) cc_final: 0.6569 (mmt90) REVERT: p 5 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7094 (ppt-90) REVERT: p 35 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8050 (ttp-110) REVERT: p 51 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7806 (ptp-170) REVERT: q 13 SER cc_start: 0.8683 (m) cc_final: 0.8040 (t) outliers start: 97 outliers final: 45 residues processed: 259 average time/residue: 1.6496 time to fit residues: 531.7355 Evaluate side-chains 238 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 73 SER Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 35 ARG Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 182 optimal weight: 0.0000 chunk 233 optimal weight: 0.0270 chunk 181 optimal weight: 0.3980 chunk 269 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 319 optimal weight: 0.5980 chunk 199 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS h 37 ASN ** q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.8145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 51470 Z= 0.117 Angle : 0.495 12.144 77120 Z= 0.251 Chirality : 0.029 0.224 9873 Planarity : 0.004 0.062 4069 Dihedral : 23.455 179.732 25977 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.47 % Allowed : 31.39 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.74 (0.19), residues: 1800 helix: -1.86 (0.21), residues: 547 sheet: -0.61 (0.34), residues: 236 loop : -2.14 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 200 HIS 0.005 0.001 HIS o 46 PHE 0.010 0.001 PHE A 146 TYR 0.015 0.001 TYR c 41 ARG 0.012 0.001 ARG g 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5957 (mmm) cc_final: 0.5618 (mmm) REVERT: A 111 ARG cc_start: 0.2316 (OUTLIER) cc_final: 0.1360 (tpp-160) REVERT: A 165 MET cc_start: -0.2109 (ppp) cc_final: -0.3420 (ppp) REVERT: A 257 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2419 (tm) REVERT: c 17 TRP cc_start: 0.5390 (m100) cc_final: 0.4578 (m-90) REVERT: c 41 TYR cc_start: 0.7388 (t80) cc_final: 0.7144 (t80) REVERT: c 45 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5909 (pp20) REVERT: c 129 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.3660 (p90) REVERT: c 182 ASP cc_start: 0.7354 (p0) cc_final: 0.6957 (p0) REVERT: d 58 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: e 31 SER cc_start: 0.8924 (m) cc_final: 0.8548 (t) REVERT: g 9 ARG cc_start: 0.2238 (mtt180) cc_final: 0.0863 (ttt180) REVERT: g 110 ARG cc_start: 0.3495 (tpt170) cc_final: 0.2909 (mtp-110) REVERT: g 143 MET cc_start: 0.1052 (ppp) cc_final: -0.0419 (mtt) REVERT: l 43 LYS cc_start: 0.8228 (mttt) cc_final: 0.7853 (tppt) REVERT: o 26 GLU cc_start: 0.5426 (mp0) cc_final: 0.5207 (mp0) REVERT: o 53 ARG cc_start: 0.7689 (mtp-110) cc_final: 0.6484 (mmp-170) REVERT: o 63 ARG cc_start: 0.7398 (mmp80) cc_final: 0.6490 (mpt-90) REVERT: o 74 ASP cc_start: 0.5903 (t0) cc_final: 0.4986 (p0) REVERT: q 13 SER cc_start: 0.8427 (m) cc_final: 0.7763 (t) REVERT: t 9 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.5790 (mmt180) outliers start: 53 outliers final: 22 residues processed: 240 average time/residue: 1.6434 time to fit residues: 490.7273 Evaluate side-chains 201 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain t residue 3 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 6.9990 chunk 127 optimal weight: 50.0000 chunk 190 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 217 optimal weight: 0.0770 chunk 157 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 250 optimal weight: 40.0000 overall best weight: 6.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN f 55 HIS ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.8959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 51470 Z= 0.380 Angle : 0.690 11.480 77120 Z= 0.344 Chirality : 0.037 0.534 9873 Planarity : 0.005 0.059 4069 Dihedral : 23.790 179.920 25977 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.67 % Favored : 92.28 % Rotamer: Outliers : 4.91 % Allowed : 30.60 % Favored : 64.48 % 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: -3.02 (0.18), residues: 1800 helix: -2.10 (0.20), residues: 550 sheet: -0.83 (0.34), residues: 239 loop : -2.30 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 102 HIS 0.007 0.002 HIS f 55 PHE 0.043 0.002 PHE f 8 TYR 0.028 0.002 TYR f 59 ARG 0.010 0.001 ARG o 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 198 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5940 (mmm) cc_final: 0.5586 (mmm) REVERT: A 219 LYS cc_start: 0.3445 (ptpt) cc_final: 0.2697 (pptt) REVERT: A 257 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2190 (tm) REVERT: c 17 TRP cc_start: 0.5488 (m100) cc_final: 0.4730 (m-90) REVERT: c 45 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6101 (pp20) REVERT: c 54 ILE cc_start: 0.6524 (OUTLIER) cc_final: 0.6293 (pp) REVERT: c 129 PHE cc_start: 0.5127 (OUTLIER) cc_final: 0.4270 (p90) REVERT: c 182 ASP cc_start: 0.7606 (p0) cc_final: 0.6995 (p0) REVERT: d 58 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: d 182 LYS cc_start: 0.8496 (tmtt) cc_final: 0.8155 (tttp) REVERT: e 31 SER cc_start: 0.8907 (m) cc_final: 0.8581 (t) REVERT: e 151 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7852 (pmm) REVERT: f 44 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7236 (ptm160) REVERT: g 9 ARG cc_start: 0.2684 (mtt180) cc_final: 0.1092 (ttt180) REVERT: g 110 ARG cc_start: 0.3354 (tpt170) cc_final: 0.2769 (mtp-110) REVERT: g 143 MET cc_start: 0.1482 (ppp) cc_final: -0.0158 (mtt) REVERT: h 59 GLU cc_start: 0.7843 (mp0) cc_final: 0.7637 (mp0) REVERT: l 43 LYS cc_start: 0.8399 (mttt) cc_final: 0.8092 (tppt) REVERT: l 75 GLU cc_start: 0.8233 (mm-30) cc_final: 0.8014 (mm-30) REVERT: m 75 MET cc_start: 0.3682 (tmm) cc_final: 0.3427 (tmm) REVERT: o 53 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.6745 (mmp-170) REVERT: o 63 ARG cc_start: 0.7569 (mmp80) cc_final: 0.6648 (mmt90) REVERT: p 5 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.6990 (ppt-90) REVERT: q 13 SER cc_start: 0.8687 (m) cc_final: 0.8070 (t) REVERT: q 80 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8261 (tptt) outliers start: 75 outliers final: 43 residues processed: 254 average time/residue: 1.6550 time to fit residues: 523.8695 Evaluate side-chains 241 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 180 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 80 LYS Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 40.0000 chunk 233 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 268 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 296 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS g 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.9028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51470 Z= 0.190 Angle : 0.540 11.987 77120 Z= 0.275 Chirality : 0.031 0.206 9873 Planarity : 0.004 0.065 4069 Dihedral : 23.687 179.809 25977 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.60 % Allowed : 32.77 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.19), residues: 1800 helix: -1.86 (0.21), residues: 550 sheet: -0.80 (0.34), residues: 238 loop : -2.21 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 200 HIS 0.010 0.001 HIS f 55 PHE 0.010 0.001 PHE p 32 TYR 0.015 0.001 TYR r 69 ARG 0.008 0.001 ARG e 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5920 (mmm) cc_final: 0.5553 (mmm) REVERT: A 50 ARG cc_start: 0.2674 (OUTLIER) cc_final: 0.1483 (mmm160) REVERT: A 165 MET cc_start: -0.2122 (ppp) cc_final: -0.3436 (ppp) REVERT: A 219 LYS cc_start: 0.3418 (ptpt) cc_final: 0.2691 (pptt) REVERT: A 223 GLU cc_start: 0.7531 (tp30) cc_final: 0.7281 (tm-30) REVERT: A 257 LEU cc_start: 0.2751 (OUTLIER) cc_final: 0.2246 (tm) REVERT: c 2 GLN cc_start: 0.7767 (mt0) cc_final: 0.7406 (mm110) REVERT: c 17 TRP cc_start: 0.5368 (m100) cc_final: 0.4628 (m-90) REVERT: c 45 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6128 (pp20) REVERT: c 54 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6210 (pp) REVERT: c 125 ARG cc_start: 0.6492 (tpm-80) cc_final: 0.6232 (tpm-80) REVERT: c 129 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.4240 (p90) REVERT: c 182 ASP cc_start: 0.7403 (p0) cc_final: 0.6896 (p0) REVERT: d 58 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7888 (mp10) REVERT: d 182 LYS cc_start: 0.8516 (tmtt) cc_final: 0.8309 (tttt) REVERT: d 194 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7375 (pt) REVERT: e 31 SER cc_start: 0.8923 (m) cc_final: 0.8568 (t) REVERT: e 92 ARG cc_start: 0.8197 (mpp80) cc_final: 0.7939 (mtm180) REVERT: g 9 ARG cc_start: 0.2773 (mtt180) cc_final: 0.0865 (ttt-90) REVERT: g 110 ARG cc_start: 0.3627 (tpt170) cc_final: 0.2894 (mtp-110) REVERT: g 143 MET cc_start: 0.1525 (ppp) cc_final: -0.0077 (mtt) REVERT: l 43 LYS cc_start: 0.8293 (mttt) cc_final: 0.7981 (tppt) REVERT: o 53 ARG cc_start: 0.7884 (mtp-110) cc_final: 0.6642 (mmp-170) REVERT: o 63 ARG cc_start: 0.7418 (mmp80) cc_final: 0.6603 (mpt-90) REVERT: o 74 ASP cc_start: 0.6022 (t0) cc_final: 0.5538 (p0) REVERT: p 5 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7273 (ppt-90) REVERT: p 51 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7723 (ptp-170) REVERT: q 13 SER cc_start: 0.8460 (m) cc_final: 0.7785 (t) REVERT: t 9 ARG cc_start: 0.7143 (ttp-170) cc_final: 0.5758 (tpp-160) outliers start: 55 outliers final: 34 residues processed: 233 average time/residue: 1.6679 time to fit residues: 480.5609 Evaluate side-chains 234 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 303 optimal weight: 0.0980 chunk 262 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 161 optimal weight: 30.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS f 63 ASN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.9244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 51470 Z= 0.202 Angle : 0.545 12.145 77120 Z= 0.276 Chirality : 0.031 0.254 9873 Planarity : 0.004 0.066 4069 Dihedral : 23.681 179.753 25977 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.54 % Allowed : 32.77 % Favored : 63.70 % 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: -2.79 (0.19), residues: 1800 helix: -1.80 (0.21), residues: 560 sheet: -0.86 (0.34), residues: 241 loop : -2.17 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 200 HIS 0.008 0.001 HIS f 58 PHE 0.038 0.002 PHE f 8 TYR 0.027 0.002 TYR f 59 ARG 0.021 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 202 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5980 (mmm) cc_final: 0.5615 (mmm) REVERT: A 39 ARG cc_start: 0.3621 (tpp-160) cc_final: 0.3167 (tpp-160) REVERT: A 50 ARG cc_start: 0.2630 (OUTLIER) cc_final: 0.1739 (mmm160) REVERT: A 152 MET cc_start: 0.1871 (ppp) cc_final: 0.1605 (pmm) REVERT: A 219 LYS cc_start: 0.3400 (ptpt) cc_final: 0.2650 (pptt) REVERT: A 223 GLU cc_start: 0.7590 (tp30) cc_final: 0.7375 (tm-30) REVERT: A 257 LEU cc_start: 0.2788 (OUTLIER) cc_final: 0.2252 (tm) REVERT: c 2 GLN cc_start: 0.7773 (mt0) cc_final: 0.7261 (mm110) REVERT: c 17 TRP cc_start: 0.5293 (m100) cc_final: 0.4618 (m-90) REVERT: c 45 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6174 (pp20) REVERT: c 54 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6153 (pp) REVERT: c 125 ARG cc_start: 0.6540 (tpm-80) cc_final: 0.6298 (tpm-80) REVERT: c 129 PHE cc_start: 0.5274 (OUTLIER) cc_final: 0.4159 (p90) REVERT: c 182 ASP cc_start: 0.7465 (p0) cc_final: 0.6898 (p0) REVERT: d 46 ARG cc_start: 0.7646 (mmp80) cc_final: 0.6908 (ttp80) REVERT: d 58 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: d 194 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7459 (pt) REVERT: e 31 SER cc_start: 0.8919 (m) cc_final: 0.8569 (t) REVERT: e 92 ARG cc_start: 0.8204 (mpp80) cc_final: 0.7844 (mtm180) REVERT: e 146 MET cc_start: 0.7354 (ttp) cc_final: 0.7039 (ttt) REVERT: g 9 ARG cc_start: 0.2924 (mtt180) cc_final: 0.1051 (ttt-90) REVERT: g 110 ARG cc_start: 0.3442 (tpt170) cc_final: 0.2722 (mtp-110) REVERT: g 143 MET cc_start: 0.1442 (ppp) cc_final: -0.0100 (mtt) REVERT: l 37 TYR cc_start: 0.8156 (p90) cc_final: 0.7935 (p90) REVERT: l 43 LYS cc_start: 0.8274 (mttt) cc_final: 0.7959 (tppt) REVERT: o 53 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.6667 (mmp-170) REVERT: o 63 ARG cc_start: 0.7397 (mmp80) cc_final: 0.6552 (mmt90) REVERT: o 74 ASP cc_start: 0.6234 (t0) cc_final: 0.5559 (p0) REVERT: p 5 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7438 (ppt-90) REVERT: p 51 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (ptp-170) REVERT: q 13 SER cc_start: 0.8380 (m) cc_final: 0.7759 (t) REVERT: q 80 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8268 (tptm) REVERT: r 72 ARG cc_start: 0.4114 (mmm160) cc_final: 0.3853 (ptp-170) REVERT: t 9 ARG cc_start: 0.7140 (ttp-170) cc_final: 0.5727 (tpp80) outliers start: 54 outliers final: 33 residues processed: 245 average time/residue: 1.7150 time to fit residues: 518.4217 Evaluate side-chains 229 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 102 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 3 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 2 VAL Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 80 LYS Chi-restraints excluded: chain t residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 270 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.133793 restraints weight = 156018.512| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.54 r_work: 0.3721 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5282 moved from start: 0.9812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 51470 Z= 0.280 Angle : 0.614 11.973 77120 Z= 0.310 Chirality : 0.034 0.204 9873 Planarity : 0.005 0.065 4069 Dihedral : 23.898 179.921 25977 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.60 % Allowed : 32.70 % Favored : 63.70 % 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: -2.98 (0.19), residues: 1800 helix: -2.02 (0.20), residues: 578 sheet: -0.95 (0.33), residues: 243 loop : -2.25 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 200 HIS 0.007 0.001 HIS t 67 PHE 0.028 0.002 PHE h 65 TYR 0.022 0.002 TYR r 31 ARG 0.013 0.001 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11886.87 seconds wall clock time: 212 minutes 22.83 seconds (12742.83 seconds total)