Starting phenix.real_space_refine on Wed Feb 14 08:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nhv_9374/02_2024/6nhv_9374_updated.pdb" } resolution = 3.5 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= -0.001 sd= 0.934 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5653 2.51 5 N 1546 2.21 5 O 1718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 177": "OD1" <-> "OD2" Residue "R ASP 178": "OD1" <-> "OD2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "R GLU 214": "OE1" <-> "OE2" Residue "R ASP 222": "OD1" <-> "OD2" Residue "R GLU 244": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R ASP 255": "OD1" <-> "OD2" Residue "R GLU 280": "OE1" <-> "OE2" Residue "R TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 293": "OD1" <-> "OD2" Residue "R ASP 305": "OD1" <-> "OD2" Residue "R ASP 310": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1828 Unusual residues: {'CRO': 1} Classifications: {'peptide': 228, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216, None: 2} Not linked: pdbres="LEU A 64 " pdbres="CRO A 66 " Not linked: pdbres="CRO A 66 " pdbres="VAL A 68 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2251 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 290} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1107 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1107 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "X" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8948 At special positions: 0 Unit cell: (119.78, 94.34, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1718 8.00 N 1546 7.00 C 5653 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 5 sheets defined 45.9% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 76 through 81 removed outlier: 5.435A pdb=" N ARG A 80 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'N' and resid 18 through 32 removed outlier: 3.737A pdb=" N LEU N 22 " --> pdb=" O PRO N 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU N 23 " --> pdb=" O GLY N 19 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 88 removed outlier: 3.748A pdb=" N ALA N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 32 removed outlier: 3.707A pdb=" N LEU O 22 " --> pdb=" O PRO O 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU O 23 " --> pdb=" O GLY O 19 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 88 removed outlier: 3.820A pdb=" N ALA O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 44 removed outlier: 3.581A pdb=" N SER R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 40 " --> pdb=" O GLU R 36 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY R 42 " --> pdb=" O THR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 71 removed outlier: 3.628A pdb=" N GLU R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY R 68 " --> pdb=" O TYR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 97 removed outlier: 3.590A pdb=" N LEU R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 136 removed outlier: 3.581A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG R 124 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR R 131 " --> pdb=" O ARG R 127 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 174 removed outlier: 3.625A pdb=" N TYR R 145 " --> pdb=" O GLU R 141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP R 151 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS R 167 " --> pdb=" O GLU R 163 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU R 168 " --> pdb=" O GLN R 164 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 removed outlier: 3.960A pdb=" N ARG R 181 " --> pdb=" O ASP R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 207 Processing helix chain 'R' and resid 210 through 219 removed outlier: 3.711A pdb=" N CYS R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 240 Processing helix chain 'R' and resid 243 through 251 Processing helix chain 'R' and resid 266 through 273 Processing helix chain 'R' and resid 276 through 284 Processing helix chain 'R' and resid 299 through 306 Processing helix chain 'R' and resid 309 through 317 Processing helix chain 'S' and resid 25 through 44 removed outlier: 3.593A pdb=" N SER S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE S 40 " --> pdb=" O GLU S 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY S 42 " --> pdb=" O THR S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 71 removed outlier: 3.597A pdb=" N GLU S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP S 62 " --> pdb=" O GLU S 58 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY S 68 " --> pdb=" O TYR S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 97 removed outlier: 3.569A pdb=" N LEU S 88 " --> pdb=" O ILE S 84 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS S 89 " --> pdb=" O ALA S 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU S 90 " --> pdb=" O TRP S 86 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 136 removed outlier: 3.625A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR S 120 " --> pdb=" O ASP S 116 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 140 through 164 removed outlier: 3.689A pdb=" N TYR S 145 " --> pdb=" O GLU S 141 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA S 148 " --> pdb=" O ALA S 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP S 151 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE S 154 " --> pdb=" O SER S 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU S 161 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE S 162 " --> pdb=" O ARG S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 44 removed outlier: 3.623A pdb=" N SER T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE T 40 " --> pdb=" O GLU T 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY T 42 " --> pdb=" O THR T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 71 removed outlier: 3.646A pdb=" N GLU T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP T 62 " --> pdb=" O GLU T 58 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY T 68 " --> pdb=" O TYR T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 97 removed outlier: 3.573A pdb=" N LEU T 88 " --> pdb=" O ILE T 84 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU T 90 " --> pdb=" O TRP T 86 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET T 97 " --> pdb=" O ARG T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 136 removed outlier: 3.631A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG T 124 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR T 131 " --> pdb=" O ARG T 127 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG T 134 " --> pdb=" O LEU T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 164 removed outlier: 3.689A pdb=" N TYR T 145 " --> pdb=" O GLU T 141 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA T 148 " --> pdb=" O ALA T 144 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP T 151 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE T 154 " --> pdb=" O SER T 150 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG T 158 " --> pdb=" O PHE T 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU T 161 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE T 162 " --> pdb=" O ARG T 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 32 removed outlier: 3.742A pdb=" N LEU X 22 " --> pdb=" O PRO X 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU X 23 " --> pdb=" O GLY X 19 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 88 removed outlier: 3.769A pdb=" N ALA X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL X 87 " --> pdb=" O SER X 83 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 25 through 36 removed outlier: 6.297A pdb=" N LEU A 119 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLU A 17 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN A 121 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASP A 19 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 123 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ASP A 21 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 125 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS A 166 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 149 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 41 through 46 removed outlier: 6.113A pdb=" N GLN N 101 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA N 64 " --> pdb=" O GLN N 101 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER N 103 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LEU N 66 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU N 105 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE N 68 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG N 107 " --> pdb=" O ILE N 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'O' and resid 41 through 46 removed outlier: 6.136A pdb=" N GLN O 101 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA O 64 " --> pdb=" O GLN O 101 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N SER O 103 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU O 66 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLU O 105 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE O 68 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG O 107 " --> pdb=" O ILE O 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'X' and resid 41 through 46 removed outlier: 6.071A pdb=" N GLN X 101 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA X 64 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER X 103 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU X 66 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU X 105 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE X 68 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG X 107 " --> pdb=" O ILE X 68 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.50 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: 1626 1.29 - 1.42: 2012 1.42 - 1.55: 5377 1.55 - 1.68: 2 1.68 - 1.81: 50 Bond restraints: 9067 Sorted by residual: bond pdb=" C LEU R 90 " pdb=" N ILE R 91 " ideal model delta sigma weight residual 1.335 1.232 0.102 1.26e-02 6.30e+03 6.61e+01 bond pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 1.331 1.250 0.081 1.24e-02 6.50e+03 4.23e+01 bond pdb=" C LYS A 156 " pdb=" O LYS A 156 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.17e-02 7.31e+03 3.02e+01 bond pdb=" C VAL O 5 " pdb=" N ILE O 6 " ideal model delta sigma weight residual 1.330 1.262 0.068 1.25e-02 6.40e+03 2.95e+01 bond pdb=" C GLU R 81 " pdb=" N GLU R 82 " ideal model delta sigma weight residual 1.335 1.260 0.074 1.38e-02 5.25e+03 2.91e+01 ... (remaining 9062 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 169 106.88 - 113.65: 5233 113.65 - 120.42: 3559 120.42 - 127.20: 3227 127.20 - 133.97: 56 Bond angle restraints: 12244 Sorted by residual: angle pdb=" C VAL A 224 " pdb=" N THR A 225 " pdb=" CA THR A 225 " ideal model delta sigma weight residual 122.73 114.16 8.57 1.62e+00 3.81e-01 2.80e+01 angle pdb=" O PHE A 223 " pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 123.23 117.38 5.85 1.30e+00 5.92e-01 2.02e+01 angle pdb=" N ILE A 123 " pdb=" CA ILE A 123 " pdb=" C ILE A 123 " ideal model delta sigma weight residual 108.48 114.29 -5.81 1.44e+00 4.82e-01 1.63e+01 angle pdb=" N ILE R 162 " pdb=" CA ILE R 162 " pdb=" C ILE R 162 " ideal model delta sigma weight residual 110.42 114.18 -3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N VAL A 224 " ideal model delta sigma weight residual 116.01 121.67 -5.66 1.49e+00 4.50e-01 1.45e+01 ... (remaining 12239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5279 17.67 - 35.34: 157 35.34 - 53.02: 36 53.02 - 70.69: 7 70.69 - 88.36: 5 Dihedral angle restraints: 5484 sinusoidal: 2166 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.07 58.07 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PRO A 196 " pdb=" C PRO A 196 " pdb=" N ASP A 197 " pdb=" CA ASP A 197 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N THR A 97 " pdb=" CA THR A 97 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 966 0.044 - 0.088: 367 0.088 - 0.133: 89 0.133 - 0.177: 8 0.177 - 0.221: 4 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA GLU A 5 " pdb=" N GLU A 5 " pdb=" C GLU A 5 " pdb=" CB GLU A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA LYS A 41 " pdb=" N LYS A 41 " pdb=" C LYS A 41 " pdb=" CB LYS A 41 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LYS A 156 " pdb=" N LYS A 156 " pdb=" C LYS A 156 " pdb=" CB LYS A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1431 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO A 66 " -0.040 2.00e-02 2.50e+03 3.40e-02 2.90e+01 pdb=" CG2 CRO A 66 " 0.068 2.00e-02 2.50e+03 pdb=" C1 CRO A 66 " -0.033 2.00e-02 2.50e+03 pdb=" C2 CRO A 66 " -0.024 2.00e-02 2.50e+03 pdb=" CA1 CRO A 66 " 0.011 2.00e-02 2.50e+03 pdb=" CA2 CRO A 66 " -0.015 2.00e-02 2.50e+03 pdb=" CA3 CRO A 66 " 0.055 2.00e-02 2.50e+03 pdb=" N2 CRO A 66 " -0.017 2.00e-02 2.50e+03 pdb=" N3 CRO A 66 " -0.005 2.00e-02 2.50e+03 pdb=" O2 CRO A 66 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB2 CRO A 66 " 0.014 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG2 CRO A 66 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 CRO A 66 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 CRO A 66 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 CRO A 66 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 CRO A 66 " 0.016 2.00e-02 2.50e+03 pdb=" CZ CRO A 66 " -0.006 2.00e-02 2.50e+03 pdb=" OH CRO A 66 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 162 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.89e+00 pdb=" C ILE R 162 " -0.054 2.00e-02 2.50e+03 pdb=" O ILE R 162 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU R 163 " 0.018 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 151 2.68 - 3.23: 8347 3.23 - 3.79: 12701 3.79 - 4.34: 18783 4.34 - 4.90: 30645 Nonbonded interactions: 70627 Sorted by model distance: nonbonded pdb=" NH1 ARG X 77 " pdb=" OE2 GLU X 108 " model vdw 2.125 2.520 nonbonded pdb=" NH1 ARG O 77 " pdb=" OE2 GLU O 108 " model vdw 2.153 2.520 nonbonded pdb=" OD2 ASP T 62 " pdb=" OH TYR T 145 " model vdw 2.206 2.440 nonbonded pdb=" NH1 ARG N 77 " pdb=" OE2 GLU N 108 " model vdw 2.295 2.520 nonbonded pdb=" OD2 ASP R 62 " pdb=" OH TYR R 145 " model vdw 2.316 2.440 ... (remaining 70622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'X' } ncs_group { reference = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.550 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.140 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 : 0.010 0.107 9067 Z= 0.658 Angle : 0.935 8.573 12244 Z= 0.597 Chirality : 0.048 0.221 1434 Planarity : 0.006 0.072 1579 Dihedral : 9.922 88.359 3352 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.21 % Allowed : 1.83 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -3.60 (0.20), residues: 1149 helix: -4.05 (0.12), residues: 551 sheet: 0.47 (0.32), residues: 211 loop : -1.01 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 86 HIS 0.008 0.002 HIS A 169 PHE 0.017 0.002 PHE A 165 TYR 0.012 0.002 TYR A 151 ARG 0.012 0.001 ARG O 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 397 time to evaluate : 1.058 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: N 105 GLU cc_start: 0.7812 (tt0) cc_final: 0.7511 (tt0) REVERT: R 97 MET cc_start: 0.7590 (mtt) cc_final: 0.7274 (mtt) REVERT: R 211 GLU cc_start: 0.8396 (pm20) cc_final: 0.7240 (pm20) REVERT: T 67 MET cc_start: 0.7829 (mtp) cc_final: 0.7590 (mtp) outliers start: 2 outliers final: 0 residues processed: 398 average time/residue: 0.2537 time to fit residues: 132.2473 Evaluate side-chains 272 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 135 ASN A 149 ASN ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 ASN T 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9067 Z= 0.174 Angle : 0.547 10.789 12244 Z= 0.284 Chirality : 0.040 0.133 1434 Planarity : 0.005 0.047 1579 Dihedral : 4.646 56.222 1254 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.33 % Allowed : 12.89 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1149 helix: -1.64 (0.19), residues: 525 sheet: 1.01 (0.31), residues: 226 loop : -0.11 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 86 HIS 0.004 0.001 HIS A 181 PHE 0.019 0.001 PHE A 165 TYR 0.016 0.002 TYR A 200 ARG 0.006 0.001 ARG N 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8739 (p90) cc_final: 0.8532 (p90) REVERT: N 117 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7761 (ttm-80) REVERT: O 13 ARG cc_start: 0.7440 (mpp80) cc_final: 0.6940 (mtm110) REVERT: R 229 TRP cc_start: 0.7949 (m-90) cc_final: 0.7641 (m-90) REVERT: S 119 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8114 (ttp80) REVERT: S 155 LEU cc_start: 0.7992 (mm) cc_final: 0.7751 (mt) outliers start: 31 outliers final: 19 residues processed: 309 average time/residue: 0.2266 time to fit residues: 93.8818 Evaluate side-chains 276 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 100 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9067 Z= 0.159 Angle : 0.494 7.246 12244 Z= 0.258 Chirality : 0.039 0.151 1434 Planarity : 0.004 0.042 1579 Dihedral : 4.324 52.198 1254 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.08 % Allowed : 16.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1149 helix: -0.03 (0.21), residues: 526 sheet: 1.26 (0.31), residues: 226 loop : 0.11 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 86 HIS 0.003 0.001 HIS A 181 PHE 0.024 0.002 PHE A 145 TYR 0.013 0.001 TYR A 200 ARG 0.004 0.000 ARG N 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 269 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 PHE cc_start: 0.6075 (m-80) cc_final: 0.5843 (m-80) REVERT: O 13 ARG cc_start: 0.7431 (mpp80) cc_final: 0.6809 (mtm110) REVERT: R 35 ASP cc_start: 0.6700 (t0) cc_final: 0.6478 (t0) REVERT: R 176 GLN cc_start: 0.8297 (mp10) cc_final: 0.7626 (mp10) REVERT: R 203 LEU cc_start: 0.8501 (mm) cc_final: 0.8243 (mm) REVERT: R 229 TRP cc_start: 0.7927 (m-90) cc_final: 0.7568 (m-90) outliers start: 38 outliers final: 26 residues processed: 286 average time/residue: 0.2243 time to fit residues: 86.6752 Evaluate side-chains 273 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 109 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS R 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9067 Z= 0.253 Angle : 0.551 11.727 12244 Z= 0.283 Chirality : 0.041 0.130 1434 Planarity : 0.004 0.041 1579 Dihedral : 4.363 36.478 1254 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.94 % Allowed : 17.72 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1149 helix: 0.66 (0.22), residues: 531 sheet: 1.42 (0.32), residues: 227 loop : -0.07 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 86 HIS 0.005 0.001 HIS O 3 PHE 0.018 0.002 PHE A 165 TYR 0.018 0.001 TYR N 50 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 13 ARG cc_start: 0.7591 (mpp80) cc_final: 0.6738 (mtm110) REVERT: R 35 ASP cc_start: 0.6845 (t0) cc_final: 0.6460 (t0) REVERT: R 207 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.7417 (mpt180) REVERT: R 210 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7590 (mt) REVERT: R 229 TRP cc_start: 0.7981 (m-90) cc_final: 0.7639 (m-90) outliers start: 46 outliers final: 31 residues processed: 269 average time/residue: 0.2205 time to fit residues: 79.8407 Evaluate side-chains 265 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 132 VAL Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9067 Z= 0.153 Angle : 0.490 10.934 12244 Z= 0.252 Chirality : 0.039 0.126 1434 Planarity : 0.003 0.040 1579 Dihedral : 4.050 24.799 1254 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 4.83 % Allowed : 19.01 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1149 helix: 1.41 (0.22), residues: 524 sheet: 1.67 (0.33), residues: 224 loop : -0.11 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 86 HIS 0.004 0.001 HIS R 264 PHE 0.019 0.001 PHE A 165 TYR 0.015 0.001 TYR N 50 ARG 0.007 0.000 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8799 (p90) cc_final: 0.8463 (p90) REVERT: O 13 ARG cc_start: 0.7591 (mpp80) cc_final: 0.6716 (mtm110) REVERT: R 35 ASP cc_start: 0.6895 (t0) cc_final: 0.6417 (t0) REVERT: R 111 GLU cc_start: 0.6645 (mp0) cc_final: 0.6382 (mp0) REVERT: R 210 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7547 (mt) REVERT: R 229 TRP cc_start: 0.7965 (m-90) cc_final: 0.7704 (m-90) outliers start: 45 outliers final: 30 residues processed: 258 average time/residue: 0.2169 time to fit residues: 75.9028 Evaluate side-chains 254 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 ASN R 186 ASN R 231 GLN R 261 ASN R 268 HIS R 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9067 Z= 0.160 Angle : 0.480 11.228 12244 Z= 0.248 Chirality : 0.039 0.120 1434 Planarity : 0.003 0.038 1579 Dihedral : 3.941 24.259 1254 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 4.30 % Allowed : 19.23 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1149 helix: 1.74 (0.22), residues: 529 sheet: 1.68 (0.33), residues: 224 loop : -0.14 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 86 HIS 0.003 0.001 HIS A 181 PHE 0.018 0.001 PHE A 165 TYR 0.012 0.001 TYR N 50 ARG 0.008 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8797 (p90) cc_final: 0.8478 (p90) REVERT: O 13 ARG cc_start: 0.7605 (mpp80) cc_final: 0.6765 (mtm110) REVERT: R 35 ASP cc_start: 0.6881 (t0) cc_final: 0.6543 (t0) REVERT: R 111 GLU cc_start: 0.6738 (mp0) cc_final: 0.6457 (mp0) REVERT: R 210 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7521 (mt) REVERT: R 229 TRP cc_start: 0.7982 (m-90) cc_final: 0.7667 (m-90) outliers start: 40 outliers final: 30 residues processed: 253 average time/residue: 0.2211 time to fit residues: 75.7242 Evaluate side-chains 259 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 98 GLU Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 74 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 224 ASN R 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9067 Z= 0.170 Angle : 0.487 11.980 12244 Z= 0.248 Chirality : 0.039 0.126 1434 Planarity : 0.003 0.038 1579 Dihedral : 3.917 25.711 1254 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 5.37 % Allowed : 18.47 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1149 helix: 1.94 (0.22), residues: 533 sheet: 1.68 (0.33), residues: 223 loop : -0.21 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 86 HIS 0.005 0.001 HIS R 264 PHE 0.018 0.001 PHE A 165 TYR 0.010 0.001 TYR A 200 ARG 0.005 0.000 ARG O 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 234 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8800 (p90) cc_final: 0.8522 (p90) REVERT: O 13 ARG cc_start: 0.7593 (mpp80) cc_final: 0.6938 (mtm110) REVERT: O 15 GLU cc_start: 0.6474 (mm-30) cc_final: 0.6236 (tp30) REVERT: R 35 ASP cc_start: 0.6963 (t0) cc_final: 0.6538 (t0) REVERT: R 210 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7480 (mt) REVERT: R 229 TRP cc_start: 0.7969 (m-90) cc_final: 0.7646 (m-90) REVERT: S 53 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7375 (mtpp) outliers start: 50 outliers final: 36 residues processed: 260 average time/residue: 0.2053 time to fit residues: 72.7656 Evaluate side-chains 268 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 262 ILE Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 72 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 155 LEU Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS R 186 ASN R 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9067 Z= 0.316 Angle : 0.589 11.916 12244 Z= 0.300 Chirality : 0.042 0.149 1434 Planarity : 0.004 0.038 1579 Dihedral : 4.422 36.109 1254 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.37 % Allowed : 18.90 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1149 helix: 1.61 (0.22), residues: 531 sheet: 1.53 (0.34), residues: 223 loop : -0.39 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 86 HIS 0.006 0.001 HIS O 3 PHE 0.018 0.002 PHE A 165 TYR 0.013 0.002 TYR A 200 ARG 0.004 0.001 ARG N 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8853 (p90) cc_final: 0.8623 (p90) REVERT: R 35 ASP cc_start: 0.7067 (t0) cc_final: 0.6674 (t0) REVERT: R 210 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7499 (mt) REVERT: R 229 TRP cc_start: 0.8000 (m-90) cc_final: 0.7742 (m-90) REVERT: R 234 LEU cc_start: 0.7373 (tp) cc_final: 0.7082 (tp) REVERT: S 53 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7720 (mtpp) REVERT: T 95 MET cc_start: 0.7764 (tpp) cc_final: 0.6965 (ttt) outliers start: 50 outliers final: 36 residues processed: 265 average time/residue: 0.2219 time to fit residues: 79.8289 Evaluate side-chains 261 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 155 LEU Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9067 Z= 0.294 Angle : 0.604 13.641 12244 Z= 0.302 Chirality : 0.042 0.154 1434 Planarity : 0.004 0.038 1579 Dihedral : 4.583 42.600 1254 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.51 % Allowed : 20.09 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1149 helix: 1.53 (0.22), residues: 531 sheet: 1.50 (0.34), residues: 222 loop : -0.48 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP T 86 HIS 0.006 0.001 HIS A 77 PHE 0.020 0.002 PHE A 165 TYR 0.011 0.001 TYR N 50 ARG 0.003 0.000 ARG N 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 50 TYR cc_start: 0.8840 (p90) cc_final: 0.8632 (p90) REVERT: R 35 ASP cc_start: 0.7080 (t0) cc_final: 0.6642 (t0) REVERT: R 210 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7516 (mt) REVERT: R 229 TRP cc_start: 0.8061 (m-90) cc_final: 0.7733 (m-90) REVERT: S 53 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7712 (mtpp) REVERT: T 95 MET cc_start: 0.7774 (tpp) cc_final: 0.7002 (ttt) outliers start: 42 outliers final: 36 residues processed: 248 average time/residue: 0.2259 time to fit residues: 75.8833 Evaluate side-chains 261 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 224 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 117 ARG Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 97 GLU Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 155 LEU Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 242 HIS R 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9067 Z= 0.193 Angle : 0.572 15.017 12244 Z= 0.281 Chirality : 0.040 0.151 1434 Planarity : 0.003 0.038 1579 Dihedral : 4.369 40.703 1254 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.08 % Allowed : 21.70 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1149 helix: 1.77 (0.22), residues: 535 sheet: 1.55 (0.34), residues: 222 loop : -0.41 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 86 HIS 0.006 0.001 HIS R 264 PHE 0.031 0.001 PHE A 83 TYR 0.011 0.001 TYR N 50 ARG 0.004 0.000 ARG O 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 ASP cc_start: 0.6968 (t0) cc_final: 0.6719 (t0) REVERT: R 210 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7452 (mt) REVERT: R 229 TRP cc_start: 0.8008 (m-90) cc_final: 0.7698 (m-90) REVERT: S 53 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7596 (mtpp) REVERT: T 95 MET cc_start: 0.7716 (tpp) cc_final: 0.6715 (ttt) outliers start: 38 outliers final: 33 residues processed: 251 average time/residue: 0.2231 time to fit residues: 75.7191 Evaluate side-chains 267 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain R residue 49 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 131 THR Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 227 ASP Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 155 LEU Chi-restraints excluded: chain T residue 92 LEU Chi-restraints excluded: chain T residue 131 THR Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN R 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.165987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.122903 restraints weight = 11539.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.126938 restraints weight = 6094.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.129664 restraints weight = 3900.125| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9067 Z= 0.165 Angle : 0.576 14.689 12244 Z= 0.278 Chirality : 0.039 0.143 1434 Planarity : 0.003 0.039 1579 Dihedral : 4.224 36.962 1254 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.44 % Allowed : 22.56 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1149 helix: 2.02 (0.22), residues: 533 sheet: 1.61 (0.34), residues: 222 loop : -0.36 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 86 HIS 0.005 0.001 HIS R 264 PHE 0.027 0.001 PHE A 83 TYR 0.018 0.001 TYR N 50 ARG 0.011 0.000 ARG N 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.19 seconds wall clock time: 41 minutes 50.84 seconds (2510.84 seconds total)