Starting phenix.real_space_refine on Sun Mar 17 06:00:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irr_35683/03_2024/8irr_35683_neut_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 438 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5259 2.51 5 N 1424 2.21 5 O 1511 1.98 5 H 8080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 191": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 216": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 227": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 338": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16329 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 882 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1913 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4682 Unusual residues: {'CLR': 3, 'R5F': 1} Classifications: {'peptide': 282, 'undetermined': 4, 'water': 2} Link IDs: {'PTRANS': 10, 'TRANS': 271, None: 6} Not linked: pdbres="TYR R 348 " pdbres="R5F R 501 " Not linked: pdbres="R5F R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="CLR R 504 " Not linked: pdbres="CLR R 504 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " Chain breaks: 3 Time building chain proxies: 6.64, per 1000 atoms: 0.41 Number of scatterers: 16329 At special positions: 0 Unit cell: (100, 106.4, 116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1511 8.00 N 1424 7.00 C 5259 6.00 H 8080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.04 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: 12.93 Conformation dependent library (CDL) restraints added in 1.7 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 40.0% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 187 through 205 removed outlier: 3.761A pdb=" N PHE A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 22 through 50 Processing helix chain 'R' and resid 52 through 56 Processing helix chain 'R' and resid 58 through 76 removed outlier: 4.022A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 4.139A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE R 104 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 107 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU R 112 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE R 117 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG R 121 " --> pdb=" O SER R 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 124 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 3.599A pdb=" N SER R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 Processing helix chain 'R' and resid 204 through 239 Processing helix chain 'R' and resid 264 through 297 removed outlier: 3.532A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.721A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 310 through 331 removed outlier: 3.931A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 344 Processing sheet with id= A, first strand: chain 'A' and resid 214 through 218 removed outlier: 6.989A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLY A 47 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.366A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.767A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.663A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.552A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.713A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.697A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.937A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1074 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: 6.22 Time building geometry restraints manager: 13.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 8045 1.13 - 1.30: 1452 1.30 - 1.47: 3227 1.47 - 1.65: 3705 1.65 - 1.82: 75 Bond restraints: 16504 Sorted by residual: bond pdb=" C7 R5F R 501 " pdb=" C8 R5F R 501 " ideal model delta sigma weight residual 1.596 1.381 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.733 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C9 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.718 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" NH1 ARG A 191 " pdb="HH12 ARG A 191 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE R 129 " pdb=" HD2 PHE R 129 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 16499 not shown) Histogram of bond angle deviations from ideal: 88.12 - 97.53: 1 97.53 - 106.93: 628 106.93 - 116.34: 19164 116.34 - 125.74: 9532 125.74 - 135.14: 315 Bond angle restraints: 29640 Sorted by residual: angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 109.58 100.79 8.79 1.29e+00 6.01e-01 4.64e+01 angle pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " pdb=" C9 R5F R 501 " ideal model delta sigma weight residual 107.56 88.12 19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.00e+00 1.00e+00 3.64e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 109.24 119.98 -10.74 1.89e+00 2.80e-01 3.23e+01 angle pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 121.87 131.16 -9.29 1.64e+00 3.72e-01 3.21e+01 ... (remaining 29635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 7166 17.41 - 34.82: 471 34.82 - 52.23: 133 52.23 - 69.64: 157 69.64 - 87.05: 10 Dihedral angle restraints: 7937 sinusoidal: 4347 harmonic: 3590 Sorted by residual: dihedral pdb=" C ASN B 119 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta harmonic sigma weight residual -122.60 -138.21 15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N HIS B 62 " pdb=" CA HIS B 62 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 7934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1049 0.116 - 0.232: 221 0.232 - 0.348: 21 0.348 - 0.464: 4 0.464 - 0.580: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ALA B 302 " pdb=" N ALA B 302 " pdb=" C ALA B 302 " pdb=" CB ALA B 302 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1293 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 148 " 0.230 2.00e-02 2.50e+03 9.78e-02 3.82e+02 pdb=" CG TRP R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP R 148 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 148 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP R 148 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP R 148 " -0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP R 148 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 148 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 148 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP R 148 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 TRP R 148 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP R 148 " -0.136 2.00e-02 2.50e+03 pdb=" HE3 TRP R 148 " -0.154 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 148 " 0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 148 " -0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP R 148 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.185 2.00e-02 2.50e+03 6.92e-02 1.92e+02 pdb=" CG TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.083 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " -0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP B 63 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP B 63 " -0.055 2.00e-02 2.50e+03 pdb=" HE3 TRP B 63 " -0.102 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 63 " 0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 63 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP B 63 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 285 " 0.072 2.00e-02 2.50e+03 6.26e-02 1.57e+02 pdb=" CG TRP R 285 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP R 285 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP R 285 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP R 285 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP R 285 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP R 285 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 285 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 285 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP R 285 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TRP R 285 " -0.088 2.00e-02 2.50e+03 pdb=" HE1 TRP R 285 " -0.078 2.00e-02 2.50e+03 pdb=" HE3 TRP R 285 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 285 " 0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 285 " -0.145 2.00e-02 2.50e+03 pdb=" HH2 TRP R 285 " 0.060 2.00e-02 2.50e+03 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 523 2.03 - 2.67: 21033 2.67 - 3.32: 49657 3.32 - 3.96: 65641 3.96 - 4.60: 96093 Nonbonded interactions: 232947 Sorted by model distance: nonbonded pdb=" HA VAL B 315 " pdb=" HG SER B 331 " model vdw 1.388 2.270 nonbonded pdb=" HG SER N 52 " pdb=" H GLN N 53 " model vdw 1.401 2.100 nonbonded pdb="HD21 ASN A 50 " pdb=" HD3 ARG A 120 " model vdw 1.462 2.270 nonbonded pdb=" HE2 HIS B 54 " pdb=" HG SER B 72 " model vdw 1.507 2.100 nonbonded pdb=" OE2 GLU B 226 " pdb=" HH TYR N 32 " model vdw 1.626 1.850 ... (remaining 232942 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.240 Extract box with map and model: 4.290 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 54.050 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.013 0.215 8424 Z= 0.836 Angle : 1.823 19.435 11426 Z= 1.217 Chirality : 0.095 0.580 1296 Planarity : 0.016 0.124 1433 Dihedral : 12.396 87.049 3201 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1012 helix: 0.07 (0.22), residues: 410 sheet: 0.71 (0.37), residues: 189 loop : -0.94 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.029 TRP R 148 HIS 0.025 0.006 HIS B 311 PHE 0.120 0.015 PHE N 68 TYR 0.076 0.015 TYR R 194 ARG 0.009 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7065 (mm-30) REVERT: A 29 GLN cc_start: 0.8237 (tp40) cc_final: 0.7980 (tp40) REVERT: A 32 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7605 (mttt) REVERT: A 33 ASP cc_start: 0.7179 (m-30) cc_final: 0.6918 (m-30) REVERT: A 186 ASP cc_start: 0.6814 (t70) cc_final: 0.6450 (m-30) REVERT: B 44 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6893 (mm-40) REVERT: G 14 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8178 (mmtm) REVERT: R 223 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8060 (mmtm) REVERT: R 339 LYS cc_start: 0.8099 (tttm) cc_final: 0.7830 (tttp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5627 time to fit residues: 173.3531 Evaluate side-chains 173 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 32 GLN B 75 GLN G 18 GLN N 82 GLN N 84 ASN R 164 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8424 Z= 0.271 Angle : 0.640 7.268 11426 Z= 0.351 Chirality : 0.042 0.145 1296 Planarity : 0.005 0.037 1433 Dihedral : 6.599 64.766 1327 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.80 % Allowed : 5.52 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1012 helix: 1.04 (0.25), residues: 410 sheet: -0.04 (0.34), residues: 212 loop : -0.60 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 80 HIS 0.006 0.001 HIS A 212 PHE 0.029 0.002 PHE N 68 TYR 0.014 0.002 TYR B 105 ARG 0.006 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 179 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8099 (tp40) cc_final: 0.7692 (tp-100) REVERT: A 33 ASP cc_start: 0.7180 (m-30) cc_final: 0.6905 (m-30) REVERT: G 14 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8062 (mtmm) REVERT: N 6 GLU cc_start: 0.6630 (mp0) cc_final: 0.6382 (mp0) REVERT: R 105 MET cc_start: 0.8001 (ttp) cc_final: 0.7770 (ttt) REVERT: R 223 LYS cc_start: 0.8292 (mmtm) cc_final: 0.8005 (mmtm) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.5570 time to fit residues: 134.1218 Evaluate side-chains 170 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 75 GLN B 88 ASN B 155 ASN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8424 Z= 0.196 Angle : 0.536 6.336 11426 Z= 0.294 Chirality : 0.040 0.138 1296 Planarity : 0.004 0.049 1433 Dihedral : 5.845 59.692 1327 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.92 % Allowed : 8.46 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1012 helix: 1.20 (0.25), residues: 410 sheet: -0.16 (0.34), residues: 212 loop : -0.53 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 212 PHE 0.015 0.001 PHE R 288 TYR 0.010 0.001 TYR A 194 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8118 (mmm-85) cc_final: 0.7711 (mmm-85) REVERT: A 29 GLN cc_start: 0.8090 (tp40) cc_final: 0.7662 (tp-100) REVERT: A 32 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7606 (mtmm) REVERT: A 33 ASP cc_start: 0.7281 (m-30) cc_final: 0.6994 (m-30) REVERT: B 263 THR cc_start: 0.8853 (t) cc_final: 0.8605 (m) REVERT: G 14 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8014 (mtmm) REVERT: R 223 LYS cc_start: 0.8260 (mmtm) cc_final: 0.7974 (mmtm) outliers start: 17 outliers final: 15 residues processed: 178 average time/residue: 0.5962 time to fit residues: 135.9984 Evaluate side-chains 173 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 75 GLN R 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8424 Z= 0.456 Angle : 0.632 7.008 11426 Z= 0.348 Chirality : 0.044 0.159 1296 Planarity : 0.005 0.049 1433 Dihedral : 6.548 55.241 1327 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.59 % Allowed : 9.81 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.26), residues: 1012 helix: 0.86 (0.25), residues: 410 sheet: -0.62 (0.34), residues: 209 loop : -0.75 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.005 0.002 HIS A 212 PHE 0.020 0.002 PHE B 199 TYR 0.015 0.002 TYR B 105 ARG 0.005 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8048 (tp40) cc_final: 0.7605 (tp-100) REVERT: A 32 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7586 (mtmm) REVERT: A 33 ASP cc_start: 0.7330 (m-30) cc_final: 0.6974 (m-30) REVERT: A 186 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: A 198 ASP cc_start: 0.8541 (m-30) cc_final: 0.8304 (m-30) REVERT: B 263 THR cc_start: 0.8911 (t) cc_final: 0.8630 (m) REVERT: G 14 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7966 (mtmm) REVERT: R 154 ILE cc_start: 0.8495 (tp) cc_final: 0.8285 (tt) REVERT: R 223 LYS cc_start: 0.8281 (mmtm) cc_final: 0.8002 (mmtm) REVERT: R 339 LYS cc_start: 0.8154 (tttm) cc_final: 0.7927 (tttp) outliers start: 23 outliers final: 18 residues processed: 183 average time/residue: 0.5835 time to fit residues: 136.4202 Evaluate side-chains 177 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8424 Z= 0.208 Angle : 0.517 6.031 11426 Z= 0.280 Chirality : 0.040 0.139 1296 Planarity : 0.004 0.064 1433 Dihedral : 5.865 60.614 1327 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.47 % Allowed : 11.27 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1012 helix: 1.22 (0.26), residues: 411 sheet: -0.76 (0.33), residues: 217 loop : -0.66 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.004 0.001 HIS A 217 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR B 105 ARG 0.009 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7961 (tp40) cc_final: 0.7595 (tp-100) REVERT: A 32 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7476 (mtmm) REVERT: A 33 ASP cc_start: 0.7376 (m-30) cc_final: 0.6997 (m-30) REVERT: A 186 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: A 198 ASP cc_start: 0.8399 (m-30) cc_final: 0.8183 (m-30) REVERT: B 263 THR cc_start: 0.8906 (t) cc_final: 0.8662 (m) REVERT: B 314 ARG cc_start: 0.8735 (ttt180) cc_final: 0.8532 (ttm170) REVERT: G 14 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7936 (mtmm) REVERT: R 223 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7946 (mmtm) REVERT: R 339 LYS cc_start: 0.8141 (tttm) cc_final: 0.7782 (tttp) outliers start: 13 outliers final: 12 residues processed: 168 average time/residue: 0.5451 time to fit residues: 119.0396 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8424 Z= 0.198 Angle : 0.497 5.753 11426 Z= 0.270 Chirality : 0.039 0.137 1296 Planarity : 0.004 0.043 1433 Dihedral : 5.630 56.023 1327 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.92 % Allowed : 11.72 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1012 helix: 1.46 (0.26), residues: 410 sheet: -0.77 (0.34), residues: 217 loop : -0.59 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR B 105 ARG 0.008 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.222 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: A 20 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7732 (mmm-85) REVERT: A 28 LYS cc_start: 0.8417 (mttp) cc_final: 0.8130 (mttp) REVERT: A 29 GLN cc_start: 0.7949 (tp40) cc_final: 0.7612 (tp-100) REVERT: A 32 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7516 (mtmm) REVERT: A 33 ASP cc_start: 0.7365 (m-30) cc_final: 0.6988 (m-30) REVERT: A 186 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7093 (m-30) REVERT: A 198 ASP cc_start: 0.8398 (m-30) cc_final: 0.8197 (m-30) REVERT: B 263 THR cc_start: 0.8915 (t) cc_final: 0.8707 (m) REVERT: G 14 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7936 (mtmm) REVERT: R 339 LYS cc_start: 0.8151 (tttm) cc_final: 0.7788 (tttp) outliers start: 17 outliers final: 15 residues processed: 163 average time/residue: 0.5569 time to fit residues: 116.7043 Evaluate side-chains 162 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8424 Z= 0.239 Angle : 0.505 5.823 11426 Z= 0.275 Chirality : 0.040 0.137 1296 Planarity : 0.004 0.041 1433 Dihedral : 5.707 56.349 1327 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.37 % Allowed : 11.50 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1012 helix: 1.48 (0.26), residues: 410 sheet: -0.85 (0.34), residues: 217 loop : -0.58 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 212 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR B 105 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: A 28 LYS cc_start: 0.8416 (mttp) cc_final: 0.8106 (mttp) REVERT: A 29 GLN cc_start: 0.7958 (tp40) cc_final: 0.7547 (tp-100) REVERT: A 32 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7498 (mtmm) REVERT: A 33 ASP cc_start: 0.7345 (m-30) cc_final: 0.7004 (m-30) REVERT: A 35 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: A 78 LYS cc_start: 0.8609 (mttt) cc_final: 0.8174 (mttt) REVERT: A 186 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: A 198 ASP cc_start: 0.8428 (m-30) cc_final: 0.8218 (m-30) REVERT: B 263 THR cc_start: 0.8921 (t) cc_final: 0.8709 (m) REVERT: G 14 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8109 (mmmt) REVERT: G 21 MET cc_start: 0.8163 (ttp) cc_final: 0.7850 (tpt) REVERT: N 13 GLN cc_start: 0.7506 (mp10) cc_final: 0.7166 (mp10) REVERT: R 339 LYS cc_start: 0.8150 (tttm) cc_final: 0.7897 (tttp) outliers start: 21 outliers final: 18 residues processed: 163 average time/residue: 0.5503 time to fit residues: 115.7528 Evaluate side-chains 167 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8424 Z= 0.227 Angle : 0.494 5.683 11426 Z= 0.269 Chirality : 0.039 0.145 1296 Planarity : 0.004 0.041 1433 Dihedral : 5.683 58.302 1327 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 11.84 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1012 helix: 1.54 (0.26), residues: 411 sheet: -0.88 (0.34), residues: 221 loop : -0.61 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 212 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.189 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: A 20 ARG cc_start: 0.8003 (mmm-85) cc_final: 0.7748 (mmm-85) REVERT: A 29 GLN cc_start: 0.7958 (tp40) cc_final: 0.7559 (tp-100) REVERT: A 33 ASP cc_start: 0.7354 (m-30) cc_final: 0.7019 (m-30) REVERT: A 35 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: A 78 LYS cc_start: 0.8621 (mttt) cc_final: 0.8179 (mttt) REVERT: A 186 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: A 198 ASP cc_start: 0.8420 (m-30) cc_final: 0.8214 (m-30) REVERT: B 138 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 234 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: B 254 ASP cc_start: 0.8194 (t0) cc_final: 0.7992 (t0) REVERT: B 263 THR cc_start: 0.8921 (t) cc_final: 0.8708 (m) REVERT: G 14 LYS cc_start: 0.8351 (ttmt) cc_final: 0.8092 (mmmt) REVERT: G 21 MET cc_start: 0.8164 (ttp) cc_final: 0.7850 (tpt) REVERT: N 13 GLN cc_start: 0.7513 (mp10) cc_final: 0.7176 (mp10) REVERT: R 278 MET cc_start: 0.8350 (tpt) cc_final: 0.7955 (tpt) REVERT: R 339 LYS cc_start: 0.8152 (tttm) cc_final: 0.7891 (tttp) outliers start: 19 outliers final: 16 residues processed: 161 average time/residue: 0.5397 time to fit residues: 112.8061 Evaluate side-chains 167 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8424 Z= 0.152 Angle : 0.465 5.332 11426 Z= 0.251 Chirality : 0.039 0.141 1296 Planarity : 0.004 0.039 1433 Dihedral : 5.400 58.494 1327 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.92 % Allowed : 11.95 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1012 helix: 1.85 (0.26), residues: 405 sheet: -0.81 (0.34), residues: 221 loop : -0.46 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 212 PHE 0.012 0.001 PHE R 288 TYR 0.010 0.001 TYR B 105 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.268 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: A 20 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7777 (mmm-85) REVERT: A 29 GLN cc_start: 0.7912 (tp40) cc_final: 0.7428 (tp-100) REVERT: A 33 ASP cc_start: 0.7344 (m-30) cc_final: 0.6998 (m-30) REVERT: A 35 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: A 78 LYS cc_start: 0.8598 (mttt) cc_final: 0.8171 (mttt) REVERT: A 186 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: A 198 ASP cc_start: 0.8399 (m-30) cc_final: 0.8191 (m-30) REVERT: B 138 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: B 254 ASP cc_start: 0.8174 (t0) cc_final: 0.7970 (t0) REVERT: G 14 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8089 (mmmt) REVERT: G 21 MET cc_start: 0.8178 (ttp) cc_final: 0.7832 (tpt) REVERT: N 13 GLN cc_start: 0.7493 (mp10) cc_final: 0.7149 (mp10) REVERT: R 339 LYS cc_start: 0.8149 (tttm) cc_final: 0.7775 (tttp) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.5657 time to fit residues: 118.1673 Evaluate side-chains 161 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8424 Z= 0.397 Angle : 0.567 6.380 11426 Z= 0.312 Chirality : 0.042 0.157 1296 Planarity : 0.004 0.040 1433 Dihedral : 6.047 55.248 1327 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.14 % Allowed : 11.72 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.27), residues: 1012 helix: 1.36 (0.26), residues: 410 sheet: -1.03 (0.34), residues: 223 loop : -0.67 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.002 PHE B 199 TYR 0.014 0.002 TYR A 194 ARG 0.004 0.001 ARG A 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8010 (tp40) cc_final: 0.7754 (tp-100) REVERT: A 33 ASP cc_start: 0.7420 (m-30) cc_final: 0.7078 (m-30) REVERT: A 35 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: A 78 LYS cc_start: 0.8632 (mttt) cc_final: 0.8212 (mttt) REVERT: A 186 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: A 198 ASP cc_start: 0.8491 (m-30) cc_final: 0.8236 (m-30) REVERT: B 234 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: G 14 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8084 (mmmt) REVERT: G 21 MET cc_start: 0.8222 (ttp) cc_final: 0.7873 (tpt) REVERT: N 13 GLN cc_start: 0.7542 (mp10) cc_final: 0.7190 (mp10) REVERT: R 339 LYS cc_start: 0.8153 (tttm) cc_final: 0.7898 (tttp) outliers start: 19 outliers final: 16 residues processed: 162 average time/residue: 0.5505 time to fit residues: 115.0699 Evaluate side-chains 166 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 201 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109490 restraints weight = 27797.632| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.17 r_work: 0.3100 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8424 Z= 0.224 Angle : 0.502 5.819 11426 Z= 0.274 Chirality : 0.040 0.147 1296 Planarity : 0.004 0.066 1433 Dihedral : 5.698 57.638 1327 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.14 % Allowed : 12.40 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1012 helix: 1.63 (0.26), residues: 405 sheet: -0.99 (0.34), residues: 221 loop : -0.52 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 212 PHE 0.019 0.001 PHE R 297 TYR 0.011 0.001 TYR B 105 ARG 0.010 0.001 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.85 seconds wall clock time: 77 minutes 30.81 seconds (4650.81 seconds total)