Starting phenix.real_space_refine on Tue Jun 25 15:08:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999_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/8v6u_42999/06_2024/8v6u_42999_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6u_42999/06_2024/8v6u_42999_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= 0.001 sd= 0.018 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 53 5.16 5 C 5264 2.51 5 N 1389 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 102": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1999 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1656 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2466 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'YEQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.62, per 1000 atoms: 0.68 Number of scatterers: 8211 At special positions: 0 Unit cell: (90.272, 118.048, 132.804, 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 53 16.00 O 1505 8.00 N 1389 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 34.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 79 through 101 Processing helix chain 'A' and resid 110 through 126 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 145 through 178 removed outlier: 3.786A pdb=" N CYS A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 149 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 150 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TRP A 151 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 190 through 206 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 318 through 348 removed outlier: 3.501A pdb=" N MET A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.580A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.634A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.611A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.617A pdb=" N ASP B 124 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 126 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 130 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 184 through 204 removed outlier: 4.134A pdb=" N ARG B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 removed outlier: 3.978A pdb=" N ILE B 227 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS B 232 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 234 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 235 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 240 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 242 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.635A pdb=" N ALA C 11 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 16 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 18 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 20 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 23 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'D' and resid 12 through 22 removed outlier: 4.256A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 211 through 215 removed outlier: 7.288A pdb=" N VAL B 139 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS B 214 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 141 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.911A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.743A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.965A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.615A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 289 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.841A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.167A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.840A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 214 through 219 removed outlier: 5.907A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 864 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: 2.56 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2136 1.33 - 1.46: 1841 1.46 - 1.59: 4326 1.59 - 1.71: 1 1.71 - 1.84: 78 Bond restraints: 8382 Sorted by residual: bond pdb=" C02 YEQ A 501 " pdb=" N03 YEQ A 501 " ideal model delta sigma weight residual 1.454 1.209 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C06 YEQ A 501 " pdb=" C07 YEQ A 501 " ideal model delta sigma weight residual 1.500 1.422 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C07 YEQ A 501 " pdb=" C08 YEQ A 501 " ideal model delta sigma weight residual 1.536 1.610 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" CZ ARG E 98 " pdb=" NH2 ARG E 98 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.73e+00 bond pdb=" CZ ARG E 179 " pdb=" NH2 ARG E 179 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.75e+00 ... (remaining 8377 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.58: 160 105.58 - 112.91: 4007 112.91 - 120.23: 3828 120.23 - 127.56: 3318 127.56 - 134.89: 87 Bond angle restraints: 11400 Sorted by residual: angle pdb=" CA ASP C 186 " pdb=" CB ASP C 186 " pdb=" CG ASP C 186 " ideal model delta sigma weight residual 112.60 121.20 -8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" C PHE E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 120.29 130.02 -9.73 1.42e+00 4.96e-01 4.70e+01 angle pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " ideal model delta sigma weight residual 112.60 119.28 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE E 68 " pdb=" CB PHE E 68 " pdb=" CG PHE E 68 " ideal model delta sigma weight residual 113.80 119.57 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.11: 4563 20.11 - 40.21: 283 40.21 - 60.31: 47 60.31 - 80.42: 9 80.42 - 100.52: 7 Dihedral angle restraints: 4909 sinusoidal: 1752 harmonic: 3157 Sorted by residual: dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER E 52 " pdb=" C SER E 52 " pdb=" N SER E 53 " pdb=" CA SER E 53 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR C 165 " pdb=" C THR C 165 " pdb=" N CYS C 166 " pdb=" CA CYS C 166 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 4906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1125 0.118 - 0.237: 190 0.237 - 0.355: 13 0.355 - 0.474: 6 0.474 - 0.592: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" C02 YEQ A 501 " pdb=" C01 YEQ A 501 " pdb=" C16 YEQ A 501 " pdb=" N03 YEQ A 501 " both_signs ideal model delta sigma weight residual False 2.61 2.02 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA PHE C 292 " pdb=" N PHE C 292 " pdb=" C PHE C 292 " pdb=" CB PHE C 292 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA THR C 164 " pdb=" N THR C 164 " pdb=" C THR C 164 " pdb=" CB THR C 164 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 1332 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.138 2.00e-02 2.50e+03 7.53e-02 1.42e+02 pdb=" CG TRP C 332 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 94 " -0.121 2.00e-02 2.50e+03 6.85e-02 9.39e+01 pdb=" CG TYR E 94 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 94 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 94 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR E 94 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 94 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 82 " -0.120 2.00e-02 2.50e+03 5.71e-02 8.15e+01 pdb=" CG TRP C 82 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 82 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP C 82 " 0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP C 82 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 82 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 82 " -0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 82 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 82 " -0.051 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 13 2.58 - 3.16: 6112 3.16 - 3.74: 11820 3.74 - 4.32: 16428 4.32 - 4.90: 28267 Nonbonded interactions: 62640 Sorted by model distance: nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR B 243 " model vdw 1.999 2.440 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.212 2.440 nonbonded pdb=" O ILE A 197 " pdb=" OG1 THR A 201 " model vdw 2.337 2.440 nonbonded pdb=" O SER A 219 " pdb=" OG SER A 219 " model vdw 2.464 2.440 nonbonded pdb=" C06 YEQ A 501 " pdb=" C15 YEQ A 501 " model vdw 2.499 2.992 ... (remaining 62635 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.000 Extract box with map and model: 11.880 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.011 0.245 8382 Z= 0.759 Angle : 1.668 12.786 11400 Z= 1.100 Chirality : 0.088 0.592 1335 Planarity : 0.012 0.115 1432 Dihedral : 14.255 100.521 2861 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 11.53 % Favored : 87.16 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1064 helix: 0.58 (0.27), residues: 349 sheet: 1.45 (0.34), residues: 222 loop : -0.48 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.018 TRP C 332 HIS 0.015 0.004 HIS C 62 PHE 0.068 0.008 PHE C 151 TYR 0.121 0.016 TYR E 94 ARG 0.005 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.818 Fit side-chains REVERT: A 208 MET cc_start: 0.7086 (mmm) cc_final: 0.6841 (mmm) REVERT: A 242 SER cc_start: 0.8572 (p) cc_final: 0.8240 (p) REVERT: B 22 ASN cc_start: 0.7935 (t0) cc_final: 0.7673 (m110) REVERT: B 200 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7390 (tt) REVERT: C 35 ASN cc_start: 0.7678 (t0) cc_final: 0.7068 (m-40) REVERT: C 156 GLN cc_start: 0.8643 (mt0) cc_final: 0.8419 (mt0) REVERT: C 333 ASP cc_start: 0.7362 (p0) cc_final: 0.7067 (p0) REVERT: E 215 TYR cc_start: 0.7622 (m-80) cc_final: 0.7350 (m-80) outliers start: 11 outliers final: 9 residues processed: 161 average time/residue: 1.1329 time to fit residues: 194.2612 Evaluate side-chains 115 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 146 GLN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8382 Z= 0.193 Angle : 0.588 6.588 11400 Z= 0.315 Chirality : 0.044 0.161 1335 Planarity : 0.004 0.037 1432 Dihedral : 7.914 90.886 1188 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.16 % Allowed : 16.17 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.66 (0.25), residues: 1064 helix: 0.71 (0.28), residues: 348 sheet: 1.29 (0.31), residues: 269 loop : -0.23 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.007 0.002 HIS B 209 PHE 0.014 0.002 PHE B 192 TYR 0.013 0.001 TYR E 178 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 0.927 Fit side-chains REVERT: A 242 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 10 LYS cc_start: 0.6529 (tttm) cc_final: 0.6179 (mtmm) REVERT: B 80 ASN cc_start: 0.7113 (p0) cc_final: 0.6791 (p0) REVERT: B 95 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7517 (mmtt) REVERT: C 35 ASN cc_start: 0.7733 (t0) cc_final: 0.7096 (m-40) REVERT: C 146 LEU cc_start: 0.8130 (mp) cc_final: 0.7881 (mt) REVERT: C 156 GLN cc_start: 0.8820 (mt0) cc_final: 0.8465 (mt0) REVERT: C 315 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8262 (m) REVERT: C 333 ASP cc_start: 0.7223 (p0) cc_final: 0.6837 (p0) outliers start: 35 outliers final: 13 residues processed: 146 average time/residue: 0.9942 time to fit residues: 155.7919 Evaluate side-chains 122 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 98 GLN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8382 Z= 0.249 Angle : 0.596 7.942 11400 Z= 0.313 Chirality : 0.044 0.164 1335 Planarity : 0.004 0.034 1432 Dihedral : 7.313 89.597 1179 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.64 % Allowed : 18.43 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.33 (0.25), residues: 1064 helix: 0.41 (0.28), residues: 357 sheet: 0.99 (0.31), residues: 271 loop : -0.34 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.007 0.002 HIS B 209 PHE 0.017 0.002 PHE C 235 TYR 0.019 0.002 TYR E 178 ARG 0.006 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 0.934 Fit side-chains REVERT: A 99 VAL cc_start: 0.7963 (t) cc_final: 0.7750 (t) REVERT: B 10 LYS cc_start: 0.6541 (tttm) cc_final: 0.6264 (mtmt) REVERT: B 24 ARG cc_start: 0.7716 (ttp-110) cc_final: 0.7182 (ttp-110) REVERT: C 35 ASN cc_start: 0.7745 (t0) cc_final: 0.7317 (t0) REVERT: C 146 LEU cc_start: 0.8318 (mp) cc_final: 0.8044 (mt) REVERT: C 156 GLN cc_start: 0.8819 (mt0) cc_final: 0.8451 (mt0) REVERT: C 217 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7725 (ppp) outliers start: 39 outliers final: 23 residues processed: 139 average time/residue: 0.9686 time to fit residues: 144.9245 Evaluate side-chains 131 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 98 GLN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8382 Z= 0.221 Angle : 0.558 7.247 11400 Z= 0.291 Chirality : 0.043 0.160 1335 Planarity : 0.004 0.032 1432 Dihedral : 7.117 87.758 1178 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.80 % Allowed : 19.98 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.23 (0.25), residues: 1064 helix: 0.49 (0.28), residues: 356 sheet: 0.98 (0.30), residues: 272 loop : -0.59 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.006 0.002 HIS B 209 PHE 0.015 0.002 PHE C 199 TYR 0.017 0.001 TYR E 178 ARG 0.012 0.001 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.903 Fit side-chains REVERT: B 10 LYS cc_start: 0.6505 (tttm) cc_final: 0.6283 (mtmt) REVERT: B 24 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7136 (ttp-110) REVERT: B 126 LYS cc_start: 0.8484 (tppt) cc_final: 0.7770 (ptpt) REVERT: C 35 ASN cc_start: 0.7787 (t0) cc_final: 0.7381 (t0) REVERT: C 156 GLN cc_start: 0.8816 (mt0) cc_final: 0.8527 (mt0) REVERT: C 217 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7712 (ppp) outliers start: 32 outliers final: 21 residues processed: 134 average time/residue: 1.0478 time to fit residues: 150.5380 Evaluate side-chains 134 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS B 98 GLN C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8382 Z= 0.280 Angle : 0.595 8.516 11400 Z= 0.310 Chirality : 0.044 0.159 1335 Planarity : 0.004 0.037 1432 Dihedral : 7.228 88.562 1178 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.23 % Allowed : 20.81 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.04 (0.25), residues: 1064 helix: 0.34 (0.28), residues: 361 sheet: 0.69 (0.29), residues: 281 loop : -0.75 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.007 0.002 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.020 0.002 TYR E 178 ARG 0.004 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 0.951 Fit side-chains REVERT: A 255 PHE cc_start: 0.7589 (t80) cc_final: 0.7085 (m-80) REVERT: B 10 LYS cc_start: 0.6655 (tttm) cc_final: 0.6403 (mtmm) REVERT: B 24 ARG cc_start: 0.7692 (ttp-110) cc_final: 0.7120 (ttp-110) REVERT: C 35 ASN cc_start: 0.7810 (t0) cc_final: 0.7440 (t0) REVERT: C 146 LEU cc_start: 0.8420 (mp) cc_final: 0.8130 (mt) REVERT: C 156 GLN cc_start: 0.8820 (mt0) cc_final: 0.8538 (mt0) outliers start: 44 outliers final: 26 residues processed: 144 average time/residue: 0.9686 time to fit residues: 149.9781 Evaluate side-chains 134 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8382 Z= 0.194 Angle : 0.541 7.249 11400 Z= 0.283 Chirality : 0.043 0.249 1335 Planarity : 0.004 0.031 1432 Dihedral : 6.990 86.325 1178 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.28 % Allowed : 22.24 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.01 (0.25), residues: 1064 helix: 0.53 (0.28), residues: 358 sheet: 0.69 (0.29), residues: 281 loop : -0.83 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.014 0.001 PHE C 199 TYR 0.015 0.001 TYR E 178 ARG 0.003 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.918 Fit side-chains REVERT: A 341 ILE cc_start: 0.7503 (mm) cc_final: 0.7018 (tp) REVERT: B 8 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: B 24 ARG cc_start: 0.7705 (ttp-110) cc_final: 0.7104 (ttp-110) REVERT: B 200 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7213 (mt) REVERT: C 35 ASN cc_start: 0.7810 (t0) cc_final: 0.7458 (t0) REVERT: C 132 ASN cc_start: 0.8079 (m-40) cc_final: 0.7305 (p0) REVERT: C 134 ARG cc_start: 0.7092 (ptt-90) cc_final: 0.6852 (ptt-90) REVERT: C 156 GLN cc_start: 0.8810 (mt0) cc_final: 0.8484 (mt0) REVERT: C 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7676 (ppp) outliers start: 36 outliers final: 19 residues processed: 138 average time/residue: 0.9933 time to fit residues: 147.4552 Evaluate side-chains 126 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8382 Z= 0.205 Angle : 0.542 6.906 11400 Z= 0.285 Chirality : 0.043 0.197 1335 Planarity : 0.004 0.032 1432 Dihedral : 6.886 84.235 1178 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.04 % Allowed : 23.07 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.01 (0.25), residues: 1064 helix: 0.48 (0.29), residues: 362 sheet: 0.68 (0.29), residues: 279 loop : -0.82 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 PHE 0.028 0.002 PHE A 255 TYR 0.016 0.001 TYR E 178 ARG 0.006 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.936 Fit side-chains REVERT: A 255 PHE cc_start: 0.7638 (t80) cc_final: 0.7081 (m-80) REVERT: A 341 ILE cc_start: 0.7494 (mm) cc_final: 0.7023 (tp) REVERT: B 24 ARG cc_start: 0.7675 (ttp-110) cc_final: 0.7084 (ttp-110) REVERT: B 200 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7240 (mt) REVERT: C 35 ASN cc_start: 0.7885 (t0) cc_final: 0.7545 (t0) REVERT: C 132 ASN cc_start: 0.8026 (m-40) cc_final: 0.7342 (p0) REVERT: C 156 GLN cc_start: 0.8811 (mt0) cc_final: 0.8493 (mt0) outliers start: 34 outliers final: 23 residues processed: 131 average time/residue: 1.0100 time to fit residues: 142.0996 Evaluate side-chains 129 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8382 Z= 0.253 Angle : 0.585 7.844 11400 Z= 0.304 Chirality : 0.044 0.183 1335 Planarity : 0.004 0.031 1432 Dihedral : 6.985 84.455 1178 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.92 % Allowed : 23.66 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.16 (0.25), residues: 1064 helix: 0.37 (0.28), residues: 362 sheet: 0.55 (0.29), residues: 281 loop : -0.90 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.006 0.002 HIS B 209 PHE 0.024 0.002 PHE A 255 TYR 0.019 0.002 TYR E 178 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 0.905 Fit side-chains REVERT: A 255 PHE cc_start: 0.7644 (t80) cc_final: 0.7081 (m-80) REVERT: B 24 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7095 (ttp-110) REVERT: B 200 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7283 (mt) REVERT: C 35 ASN cc_start: 0.7887 (t0) cc_final: 0.7568 (t0) REVERT: C 132 ASN cc_start: 0.8027 (m-40) cc_final: 0.7440 (p0) REVERT: C 146 LEU cc_start: 0.8425 (mp) cc_final: 0.8120 (mt) REVERT: C 156 GLN cc_start: 0.8818 (mt0) cc_final: 0.8503 (mt0) REVERT: C 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7660 (ppp) outliers start: 33 outliers final: 22 residues processed: 132 average time/residue: 1.0192 time to fit residues: 144.5050 Evaluate side-chains 131 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8382 Z= 0.244 Angle : 0.577 9.559 11400 Z= 0.301 Chirality : 0.044 0.173 1335 Planarity : 0.004 0.032 1432 Dihedral : 6.938 83.873 1178 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 24.49 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.17 (0.25), residues: 1064 helix: 0.45 (0.29), residues: 358 sheet: 0.52 (0.29), residues: 282 loop : -0.97 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 PHE 0.023 0.002 PHE A 255 TYR 0.018 0.002 TYR E 178 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.910 Fit side-chains REVERT: A 255 PHE cc_start: 0.7634 (t80) cc_final: 0.7071 (m-80) REVERT: B 24 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7087 (ttp-110) REVERT: B 200 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7286 (mt) REVERT: C 35 ASN cc_start: 0.7938 (t0) cc_final: 0.7633 (t0) REVERT: C 132 ASN cc_start: 0.7997 (m-40) cc_final: 0.7443 (p0) REVERT: C 156 GLN cc_start: 0.8814 (mt0) cc_final: 0.8500 (mt0) REVERT: C 217 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7654 (ppp) REVERT: C 270 ILE cc_start: 0.7746 (mm) cc_final: 0.7472 (mt) outliers start: 28 outliers final: 22 residues processed: 123 average time/residue: 1.0483 time to fit residues: 138.4802 Evaluate side-chains 128 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.0170 chunk 68 optimal weight: 0.2980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8382 Z= 0.206 Angle : 0.553 8.226 11400 Z= 0.290 Chirality : 0.043 0.166 1335 Planarity : 0.004 0.032 1432 Dihedral : 6.779 81.010 1178 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.45 % Allowed : 24.49 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.13 (0.25), residues: 1064 helix: 0.49 (0.29), residues: 358 sheet: 0.60 (0.29), residues: 280 loop : -0.99 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 PHE 0.022 0.002 PHE A 255 TYR 0.015 0.001 TYR E 178 ARG 0.007 0.000 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.854 Fit side-chains REVERT: A 255 PHE cc_start: 0.7634 (t80) cc_final: 0.7060 (m-80) REVERT: A 341 ILE cc_start: 0.7495 (mm) cc_final: 0.7062 (tp) REVERT: B 24 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7089 (ttp-110) REVERT: B 200 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7298 (mt) REVERT: C 32 GLN cc_start: 0.7919 (tt0) cc_final: 0.7499 (pt0) REVERT: C 35 ASN cc_start: 0.7885 (t0) cc_final: 0.7637 (t0) REVERT: C 132 ASN cc_start: 0.8000 (m-40) cc_final: 0.7584 (p0) REVERT: C 156 GLN cc_start: 0.8809 (mt0) cc_final: 0.8497 (mt0) REVERT: C 217 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7549 (ppp) REVERT: C 270 ILE cc_start: 0.7713 (mm) cc_final: 0.7482 (mt) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 1.0832 time to fit residues: 140.4166 Evaluate side-chains 124 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098442 restraints weight = 15540.136| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.80 r_work: 0.3338 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8382 Z= 0.286 Angle : 0.605 8.382 11400 Z= 0.315 Chirality : 0.045 0.169 1335 Planarity : 0.004 0.033 1432 Dihedral : 6.947 82.471 1178 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 24.85 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1064 helix: 0.29 (0.28), residues: 362 sheet: 0.49 (0.29), residues: 282 loop : -0.99 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.006 0.002 HIS B 209 PHE 0.023 0.002 PHE A 255 TYR 0.020 0.002 TYR E 178 ARG 0.007 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3278.04 seconds wall clock time: 58 minutes 1.40 seconds (3481.40 seconds total)