Starting phenix.real_space_refine on Thu Jan 18 10:55:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdm_31923/01_2024/7vdm_31923_updated.pdb" } resolution = 2.98 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= 0.008 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 63 5.16 5 C 5486 2.51 5 N 1438 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 222": "OE1" <-> "OE2" Residue "S PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 176": "OD1" <-> "OD2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 1": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8563 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1749 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2010 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Classifications: {'peptide': 3} Link IDs: {'PTRANS': 1, 'TRANS': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.95, per 1000 atoms: 0.58 Number of scatterers: 8563 At special positions: 0 Unit cell: (118.56, 108.16, 109.2, 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 63 16.00 O 1576 8.00 N 1438 7.00 C 5486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 31.5% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 4.003A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.784A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.570A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.906A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'R' and resid 33 through 56 Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.982A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE R 93 " --> pdb=" O TYR R 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 132 removed outlier: 4.056A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 180 through 211 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 239 through 242 No H-bonds generated for 'chain 'R' and resid 239 through 242' Processing helix chain 'R' and resid 246 through 249 No H-bonds generated for 'chain 'R' and resid 246 through 249' Processing helix chain 'R' and resid 260 through 280 Proline residue: R 276 - end of helix removed outlier: 3.530A pdb=" N TYR R 279 " --> pdb=" O ASN R 275 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.718A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.004A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.685A 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: 6.811A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.368A 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: 6.553A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.167A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A 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: 4.973A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.561A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.790A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.505A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.732A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.532A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.596A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1080 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: 2.34 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2712 1.35 - 1.48: 2341 1.48 - 1.61: 3611 1.61 - 1.75: 1 1.75 - 1.88: 87 Bond restraints: 8752 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.668 -0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.28e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.54e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 1.598 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 8747 not shown) Histogram of bond angle deviations from ideal: 93.90 - 102.77: 47 102.77 - 111.63: 3688 111.63 - 120.50: 4791 120.50 - 129.37: 3260 129.37 - 138.23: 79 Bond angle restraints: 11865 Sorted by residual: angle pdb=" CA LEU R 237 " pdb=" CB LEU R 237 " pdb=" CG LEU R 237 " ideal model delta sigma weight residual 116.30 138.23 -21.93 3.50e+00 8.16e-02 3.93e+01 angle pdb=" C ARG L 1 " pdb=" N PRO L 2 " pdb=" CA PRO L 2 " ideal model delta sigma weight residual 119.84 127.32 -7.48 1.25e+00 6.40e-01 3.58e+01 angle pdb=" CA LEU R 45 " pdb=" CB LEU R 45 " pdb=" CG LEU R 45 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.09e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N THR B 143 " pdb=" CA THR B 143 " pdb=" C THR B 143 " ideal model delta sigma weight residual 112.47 118.75 -6.28 1.24e+00 6.50e-01 2.56e+01 ... (remaining 11860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4730 17.86 - 35.72: 390 35.72 - 53.57: 52 53.57 - 71.43: 18 71.43 - 89.29: 5 Dihedral angle restraints: 5195 sinusoidal: 2035 harmonic: 3160 Sorted by residual: dihedral pdb=" CA LEU R 237 " pdb=" C LEU R 237 " pdb=" N PRO R 238 " pdb=" CA PRO R 238 " ideal model delta harmonic sigma weight residual 180.00 140.63 39.37 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 162.18 -69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -144.58 -35.42 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1051 0.074 - 0.148: 250 0.148 - 0.222: 37 0.222 - 0.295: 10 0.295 - 0.369: 3 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.75 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 1348 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 237 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.52e+01 pdb=" N PRO R 238 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO R 238 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 238 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 32 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO R 33 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO R 276 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.039 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1926 2.79 - 3.32: 7101 3.32 - 3.84: 14499 3.84 - 4.37: 16981 4.37 - 4.90: 29314 Nonbonded interactions: 69821 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.261 2.440 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.317 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.336 2.440 ... (remaining 69816 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: 0.310 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: 1.800 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.070 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.008 0.133 8752 Z= 0.511 Angle : 1.291 21.931 11865 Z= 0.678 Chirality : 0.066 0.369 1351 Planarity : 0.008 0.097 1486 Dihedral : 13.650 89.286 3148 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.22 % Allowed : 0.75 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.22), residues: 1078 helix: -2.29 (0.20), residues: 363 sheet: -0.82 (0.29), residues: 299 loop : -1.91 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 63 HIS 0.010 0.003 HIS B 142 PHE 0.028 0.003 PHE B 199 TYR 0.024 0.004 TYR R 222 ARG 0.025 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.028 Fit side-chains REVERT: A 24 ARG cc_start: 0.7023 (mtm-85) cc_final: 0.6685 (ptp-110) REVERT: A 26 ASP cc_start: 0.7134 (m-30) cc_final: 0.6880 (m-30) outliers start: 2 outliers final: 2 residues processed: 143 average time/residue: 1.3191 time to fit residues: 199.6354 Evaluate side-chains 103 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain L residue 1 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN G 18 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8752 Z= 0.280 Angle : 0.664 12.280 11865 Z= 0.335 Chirality : 0.043 0.179 1351 Planarity : 0.005 0.074 1486 Dihedral : 6.588 68.814 1250 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.80 % Allowed : 11.40 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1078 helix: -0.07 (0.26), residues: 364 sheet: -0.71 (0.29), residues: 294 loop : -1.55 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.002 HIS B 91 PHE 0.016 0.002 PHE A 223 TYR 0.027 0.002 TYR R 222 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.071 Fit side-chains REVERT: A 21 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7428 (ttm170) REVERT: A 26 ASP cc_start: 0.7269 (m-30) cc_final: 0.6985 (OUTLIER) REVERT: A 349 LYS cc_start: 0.8172 (ttmp) cc_final: 0.7966 (ttpm) REVERT: B 138 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7239 (tp30) REVERT: G 38 MET cc_start: 0.7344 (ttp) cc_final: 0.6939 (ttp) outliers start: 26 outliers final: 16 residues processed: 125 average time/residue: 1.3517 time to fit residues: 179.4723 Evaluate side-chains 121 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 306 GLN A 331 ASN A 333 GLN B 175 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8752 Z= 0.207 Angle : 0.589 10.759 11865 Z= 0.298 Chirality : 0.041 0.159 1351 Planarity : 0.004 0.069 1486 Dihedral : 5.865 69.804 1246 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.55 % Allowed : 13.66 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.61 (0.25), residues: 1078 helix: 0.92 (0.27), residues: 365 sheet: -0.66 (0.30), residues: 290 loop : -1.31 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 104 TYR 0.042 0.002 TYR R 222 ARG 0.008 0.000 ARG S 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.944 Fit side-chains REVERT: A 26 ASP cc_start: 0.7126 (m-30) cc_final: 0.6849 (OUTLIER) REVERT: A 349 LYS cc_start: 0.8100 (ttmp) cc_final: 0.7868 (ttpm) REVERT: B 323 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6901 (m-30) REVERT: G 37 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8577 (mp) REVERT: G 38 MET cc_start: 0.7312 (ttp) cc_final: 0.6921 (ttp) REVERT: R 61 ARG cc_start: 0.7546 (ptp-110) cc_final: 0.7194 (ptp-110) outliers start: 33 outliers final: 15 residues processed: 134 average time/residue: 1.2039 time to fit residues: 171.9695 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 306 GLN A 331 ASN A 333 GLN B 142 HIS B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8752 Z= 0.271 Angle : 0.614 11.013 11865 Z= 0.313 Chirality : 0.043 0.154 1351 Planarity : 0.004 0.058 1486 Dihedral : 5.735 69.740 1243 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.09 % Allowed : 15.59 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.35 (0.26), residues: 1078 helix: 1.29 (0.28), residues: 364 sheet: -0.64 (0.30), residues: 288 loop : -1.21 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 36 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.001 PHE A 223 TYR 0.033 0.002 TYR R 222 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 0.944 Fit side-chains REVERT: A 21 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7537 (ttm170) REVERT: A 26 ASP cc_start: 0.7181 (m-30) cc_final: 0.6894 (m-30) REVERT: A 349 LYS cc_start: 0.8178 (ttmp) cc_final: 0.7961 (ttpm) REVERT: B 217 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.6915 (ppp) REVERT: B 323 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: G 37 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8597 (mp) REVERT: G 38 MET cc_start: 0.7359 (ttp) cc_final: 0.6975 (ttp) REVERT: R 61 ARG cc_start: 0.7669 (ptp-110) cc_final: 0.7449 (ptp-110) REVERT: R 222 TYR cc_start: 0.6233 (p90) cc_final: 0.5082 (p90) outliers start: 38 outliers final: 19 residues processed: 134 average time/residue: 1.1930 time to fit residues: 170.6107 Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0670 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 306 GLN A 331 ASN B 142 HIS B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8752 Z= 0.202 Angle : 0.568 9.772 11865 Z= 0.289 Chirality : 0.041 0.157 1351 Planarity : 0.004 0.057 1486 Dihedral : 5.463 70.842 1243 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.76 % Allowed : 17.20 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1078 helix: 1.62 (0.28), residues: 361 sheet: -0.51 (0.31), residues: 287 loop : -1.10 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.016 0.001 HIS B 142 PHE 0.011 0.001 PHE S 200 TYR 0.031 0.002 TYR R 222 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 0.961 Fit side-chains REVERT: A 26 ASP cc_start: 0.7136 (m-30) cc_final: 0.6851 (OUTLIER) REVERT: A 349 LYS cc_start: 0.8174 (ttmp) cc_final: 0.7958 (ttpm) REVERT: B 217 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6925 (ppp) REVERT: B 323 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: G 38 MET cc_start: 0.7312 (ttp) cc_final: 0.6926 (ttp) REVERT: R 222 TYR cc_start: 0.6259 (p90) cc_final: 0.5082 (p90) outliers start: 35 outliers final: 20 residues processed: 139 average time/residue: 1.1933 time to fit residues: 176.9183 Evaluate side-chains 129 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 331 ASN B 175 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8752 Z= 0.189 Angle : 0.553 9.462 11865 Z= 0.282 Chirality : 0.041 0.159 1351 Planarity : 0.004 0.052 1486 Dihedral : 5.323 71.194 1243 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.09 % Allowed : 17.74 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.10 (0.26), residues: 1078 helix: 1.82 (0.28), residues: 360 sheet: -0.47 (0.31), residues: 288 loop : -1.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE A 196 TYR 0.030 0.002 TYR R 222 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.024 Fit side-chains REVERT: A 25 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: B 217 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6916 (ppp) REVERT: G 38 MET cc_start: 0.7257 (ttp) cc_final: 0.6893 (ttp) REVERT: R 222 TYR cc_start: 0.6308 (p90) cc_final: 0.5080 (p90) outliers start: 38 outliers final: 18 residues processed: 138 average time/residue: 1.1264 time to fit residues: 166.2769 Evaluate side-chains 126 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 306 GLN A 331 ASN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8752 Z= 0.155 Angle : 0.549 13.701 11865 Z= 0.273 Chirality : 0.041 0.163 1351 Planarity : 0.004 0.055 1486 Dihedral : 5.152 71.590 1243 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.44 % Allowed : 19.03 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.27), residues: 1078 helix: 2.10 (0.28), residues: 352 sheet: -0.40 (0.31), residues: 287 loop : -0.89 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE R 104 TYR 0.030 0.001 TYR R 222 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.982 Fit side-chains REVERT: A 313 ARG cc_start: 0.6509 (mpp80) cc_final: 0.6309 (mtm110) REVERT: B 217 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6889 (ppp) REVERT: G 38 MET cc_start: 0.7224 (ttp) cc_final: 0.6847 (ttp) REVERT: R 222 TYR cc_start: 0.6301 (p90) cc_final: 0.5066 (p90) outliers start: 32 outliers final: 18 residues processed: 135 average time/residue: 1.2025 time to fit residues: 173.1996 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 46 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 331 ASN A 333 GLN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8752 Z= 0.217 Angle : 0.587 13.753 11865 Z= 0.292 Chirality : 0.042 0.161 1351 Planarity : 0.004 0.054 1486 Dihedral : 5.283 71.547 1243 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.87 % Allowed : 18.82 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.27), residues: 1078 helix: 1.92 (0.28), residues: 360 sheet: -0.48 (0.30), residues: 294 loop : -0.87 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 154 HIS 0.006 0.001 HIS B 142 PHE 0.011 0.001 PHE A 196 TYR 0.029 0.002 TYR R 222 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.903 Fit side-chains REVERT: A 313 ARG cc_start: 0.6533 (mpp80) cc_final: 0.6308 (mtm110) REVERT: B 38 ASP cc_start: 0.7401 (m-30) cc_final: 0.7180 (m-30) REVERT: B 217 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.6936 (ppp) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: G 38 MET cc_start: 0.7261 (ttp) cc_final: 0.6888 (ttp) REVERT: R 222 TYR cc_start: 0.6310 (p90) cc_final: 0.5091 (p90) outliers start: 36 outliers final: 18 residues processed: 133 average time/residue: 1.1443 time to fit residues: 162.7088 Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 30.0000 chunk 97 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 306 GLN A 331 ASN A 333 GLN B 175 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8752 Z= 0.298 Angle : 0.654 13.921 11865 Z= 0.325 Chirality : 0.044 0.154 1351 Planarity : 0.004 0.056 1486 Dihedral : 5.603 70.050 1243 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.87 % Allowed : 19.14 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.12 (0.26), residues: 1078 helix: 1.82 (0.28), residues: 357 sheet: -0.47 (0.30), residues: 288 loop : -0.96 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 36 HIS 0.007 0.002 HIS B 142 PHE 0.014 0.002 PHE A 196 TYR 0.029 0.002 TYR R 222 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.001 Fit side-chains REVERT: A 25 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: B 217 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7023 (ppp) REVERT: B 234 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8186 (m-80) REVERT: B 323 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.6840 (m-30) outliers start: 36 outliers final: 21 residues processed: 132 average time/residue: 1.3008 time to fit residues: 183.1432 Evaluate side-chains 131 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 306 GLN A 331 ASN A 333 GLN B 175 GLN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8752 Z= 0.327 Angle : 0.676 13.964 11865 Z= 0.335 Chirality : 0.045 0.162 1351 Planarity : 0.004 0.054 1486 Dihedral : 5.735 69.279 1243 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.12 % Allowed : 20.65 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.03 (0.26), residues: 1078 helix: 1.65 (0.28), residues: 357 sheet: -0.55 (0.30), residues: 288 loop : -1.00 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 36 HIS 0.008 0.002 HIS B 142 PHE 0.014 0.002 PHE A 223 TYR 0.029 0.002 TYR R 222 ARG 0.009 0.001 ARG S 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.984 Fit side-chains REVERT: B 217 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7150 (ppp) REVERT: B 234 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: S 76 LYS cc_start: 0.7634 (tptm) cc_final: 0.7379 (tptp) REVERT: S 83 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.5532 (mpp) REVERT: R 167 PHE cc_start: 0.6833 (m-80) cc_final: 0.6028 (m-10) REVERT: R 222 TYR cc_start: 0.6303 (p90) cc_final: 0.5076 (p90) outliers start: 29 outliers final: 20 residues processed: 124 average time/residue: 1.1704 time to fit residues: 155.2809 Evaluate side-chains 126 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain R residue 122 THR Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 306 GLN B 175 GLN ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.176211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139002 restraints weight = 9183.250| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.03 r_work: 0.3282 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8752 Z= 0.287 Angle : 0.655 14.271 11865 Z= 0.323 Chirality : 0.044 0.155 1351 Planarity : 0.004 0.054 1486 Dihedral : 5.638 69.972 1243 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.33 % Allowed : 20.32 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.02 (0.26), residues: 1078 helix: 1.75 (0.28), residues: 354 sheet: -0.55 (0.30), residues: 288 loop : -0.99 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 36 HIS 0.007 0.002 HIS B 142 PHE 0.015 0.002 PHE R 50 TYR 0.028 0.002 TYR R 222 ARG 0.009 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3338.84 seconds wall clock time: 60 minutes 11.19 seconds (3611.19 seconds total)