Starting phenix.real_space_refine on Wed Aug 7 14:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zee_60026/08_2024/8zee_60026_neut.cif" } resolution = 2.9 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= 0.005 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 8 5.49 5 Mg 35 5.21 5 S 66 5.16 5 C 14044 2.51 5 N 2838 2.21 5 O 3225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "D ASP 20": "OD1" <-> "OD2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20218 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3766 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 25, 'TRANS': 456} Chain: "D" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2791 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 14, 'TRANS': 336} Chain: "E" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 277 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "H" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 561 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 239 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "T" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "V" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 224 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "X" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 242 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "C" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3368 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 24, 'TRANS': 405} Chain breaks: 2 Chain: "A" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2418 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Chain: "1" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 313 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "B" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1326 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 3, 'LMG': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 609 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 2, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'BCR': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'BCR': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'VTQ': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1244 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'SQD': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 12.50, per 1000 atoms: 0.62 Number of scatterers: 20218 At special positions: 0 Unit cell: (113.4, 136.35, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 66 16.00 P 8 15.00 Mg 35 11.99 O 3225 8.00 N 2838 7.00 C 14044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.99 Conformation dependent library (CDL) restraints added in 3.0 seconds 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3786 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 8 sheets defined 67.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'B' and resid 4 through 13 removed outlier: 4.035A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 10 " --> pdb=" O ARG B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 removed outlier: 3.582A pdb=" N LEU B 19 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.904A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.568A pdb=" N PHE B 190 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.945A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 206 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 235 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.812A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 295 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 306 through 313 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.626A pdb=" N TRP B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.131A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.332A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 164 Proline residue: D 149 - end of helix removed outlier: 4.248A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 189 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 220 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 4.060A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.439A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 9 through 15 removed outlier: 3.723A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 4.192A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 removed outlier: 3.669A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 4.102A pdb=" N TYR E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 81 Processing helix chain 'F' and resid 16 through 41 removed outlier: 3.693A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix removed outlier: 3.998A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 31 Processing helix chain 'H' and resid 32 through 35 removed outlier: 3.630A pdb=" N SER H 35 " --> pdb=" O PRO H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 35' Processing helix chain 'H' and resid 46 through 69 removed outlier: 3.652A pdb=" N MET H 50 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 24 Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 23 removed outlier: 3.742A pdb=" N VAL K 22 " --> pdb=" O PHE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 27 Processing helix chain 'K' and resid 28 through 42 removed outlier: 3.545A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.713A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 31 Proline residue: M 18 - end of helix removed outlier: 3.601A pdb=" N SER M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 3 through 18 Processing helix chain 'V' and resid 19 through 29 removed outlier: 3.892A pdb=" N VAL V 23 " --> pdb=" O GLY V 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 98 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 60 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 5.885A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 62 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.189A pdb=" N GLY C 73 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.884A pdb=" N PHE C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 170 Processing helix chain 'C' and resid 193 through 200 removed outlier: 4.004A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 203 No H-bonds generated for 'chain 'C' and resid 201 through 203' Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.549A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 313 Processing helix chain 'C' and resid 340 through 347 removed outlier: 4.309A pdb=" N THR C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.042A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 removed outlier: 3.515A pdb=" N TRP C 413 " --> pdb=" O SER C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 138 removed outlier: 4.108A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 166 removed outlier: 4.208A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.742A pdb=" N TYR A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.510A pdb=" N ASP A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 191 through 194 removed outlier: 3.558A pdb=" N MET A 194 " --> pdb=" O ASN A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.764A pdb=" N TYR A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 removed outlier: 3.626A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.573A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.584A pdb=" N GLY A 311 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 312' Processing helix chain 'A' and resid 316 through 333 Processing helix chain '1' and resid 44 through 57 removed outlier: 3.665A pdb=" N ALA 1 48 " --> pdb=" O PRO 1 44 " (cutoff:3.500A) Processing helix chain '1' and resid 62 through 78 removed outlier: 3.729A pdb=" N LEU 1 67 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Proline residue: 1 69 - end of helix removed outlier: 3.677A pdb=" N ASP 1 75 " --> pdb=" O GLN 1 71 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS 1 76 " --> pdb=" O GLN 1 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA2, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.953A pdb=" N GLY B 322 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.748A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.822A pdb=" N LEU B 370 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.507A pdb=" N LEU A 174 " --> pdb=" O VAL A 82 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2811 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: 6.02 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 5805 1.37 - 1.55: 14901 1.55 - 1.73: 69 1.73 - 1.92: 113 1.92 - 2.10: 144 Bond restraints: 21032 Sorted by residual: bond pdb=" C6 SQD C 620 " pdb=" S SQD C 620 " ideal model delta sigma weight residual 1.840 1.662 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" C7 LHG B 622 " pdb=" O7 LHG B 622 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C7 LHG B 621 " pdb=" O7 LHG B 621 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C7 LHG D 407 " pdb=" O7 LHG D 407 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C7 LHG K 103 " pdb=" O7 LHG K 103 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 ... (remaining 21027 not shown) Histogram of bond angle deviations from ideal: 84.18 - 102.77: 248 102.77 - 121.35: 22917 121.35 - 139.94: 5723 139.94 - 158.52: 38 158.52 - 177.11: 71 Bond angle restraints: 28997 Sorted by residual: angle pdb=" NB CLA B 609 " pdb="MG CLA B 609 " pdb=" ND CLA B 609 " ideal model delta sigma weight residual 176.90 158.45 18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" NB CLA C 604 " pdb="MG CLA C 604 " pdb=" ND CLA C 604 " ideal model delta sigma weight residual 176.90 158.74 18.16 3.00e+00 1.11e-01 3.66e+01 angle pdb=" NB CLA C 613 " pdb="MG CLA C 613 " pdb=" ND CLA C 613 " ideal model delta sigma weight residual 176.90 159.00 17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" NB CLA C 606 " pdb="MG CLA C 606 " pdb=" ND CLA C 606 " ideal model delta sigma weight residual 176.90 159.24 17.66 3.00e+00 1.11e-01 3.47e+01 angle pdb=" NB CLA B 604 " pdb="MG CLA B 604 " pdb=" ND CLA B 604 " ideal model delta sigma weight residual 176.90 159.27 17.63 3.00e+00 1.11e-01 3.45e+01 ... (remaining 28992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 10524 27.04 - 54.09: 696 54.09 - 81.13: 89 81.13 - 108.17: 22 108.17 - 135.21: 22 Dihedral angle restraints: 11353 sinusoidal: 5421 harmonic: 5932 Sorted by residual: dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N ASN A 298 " pdb=" CA ASN A 298 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" C3A DGD C 617 " pdb=" C1A DGD C 617 " pdb=" C2A DGD C 617 " pdb=" O1A DGD C 617 " ideal model delta sinusoidal sigma weight residual -24.22 110.99 -135.21 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C4D PHO D 412 " pdb=" CBD PHO D 412 " pdb=" CHA PHO D 412 " pdb=" CGD PHO D 412 " ideal model delta sinusoidal sigma weight residual 243.52 115.25 128.27 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 11350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2200 0.044 - 0.088: 468 0.088 - 0.132: 124 0.132 - 0.177: 8 0.177 - 0.221: 9 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C18 VTQ X 201 " pdb=" C17 VTQ X 201 " pdb=" C19 VTQ X 201 " pdb=" C20 VTQ X 201 " both_signs ideal model delta sigma weight residual False 2.57 2.79 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 LHG D 407 " pdb=" C1 LHG D 407 " pdb=" C3 LHG D 407 " pdb=" O2 LHG D 407 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" C2 LHG L 101 " pdb=" C1 LHG L 101 " pdb=" C3 LHG L 101 " pdb=" O2 LHG L 101 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2806 not shown) Planarity restraints: 3572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 411 " 0.110 2.00e-02 2.50e+03 1.04e-01 8.59e+02 pdb=" ND PHO D 411 " 0.049 2.00e-02 2.50e+03 pdb=" C1A PHO D 411 " -0.010 2.00e-02 2.50e+03 pdb=" C1B PHO D 411 " 0.054 2.00e-02 2.50e+03 pdb=" C1C PHO D 411 " 0.023 2.00e-02 2.50e+03 pdb=" C1D PHO D 411 " 0.001 2.00e-02 2.50e+03 pdb=" C2A PHO D 411 " -0.159 2.00e-02 2.50e+03 pdb=" C2B PHO D 411 " -0.092 2.00e-02 2.50e+03 pdb=" C2C PHO D 411 " 0.045 2.00e-02 2.50e+03 pdb=" C2D PHO D 411 " -0.028 2.00e-02 2.50e+03 pdb=" C3A PHO D 411 " 0.257 2.00e-02 2.50e+03 pdb=" C3B PHO D 411 " -0.115 2.00e-02 2.50e+03 pdb=" C3C PHO D 411 " 0.033 2.00e-02 2.50e+03 pdb=" C3D PHO D 411 " -0.042 2.00e-02 2.50e+03 pdb=" C4A PHO D 411 " 0.183 2.00e-02 2.50e+03 pdb=" C4B PHO D 411 " 0.013 2.00e-02 2.50e+03 pdb=" C4C PHO D 411 " -0.003 2.00e-02 2.50e+03 pdb=" C4D PHO D 411 " -0.011 2.00e-02 2.50e+03 pdb=" CAB PHO D 411 " -0.238 2.00e-02 2.50e+03 pdb=" CAC PHO D 411 " 0.045 2.00e-02 2.50e+03 pdb=" CAD PHO D 411 " -0.069 2.00e-02 2.50e+03 pdb=" CBD PHO D 411 " -0.098 2.00e-02 2.50e+03 pdb=" CHA PHO D 411 " -0.038 2.00e-02 2.50e+03 pdb=" CHB PHO D 411 " 0.118 2.00e-02 2.50e+03 pdb=" CHC PHO D 411 " 0.031 2.00e-02 2.50e+03 pdb=" CHD PHO D 411 " -0.027 2.00e-02 2.50e+03 pdb=" CMB PHO D 411 " -0.182 2.00e-02 2.50e+03 pdb=" CMC PHO D 411 " 0.083 2.00e-02 2.50e+03 pdb=" CMD PHO D 411 " -0.044 2.00e-02 2.50e+03 pdb=" NA PHO D 411 " 0.189 2.00e-02 2.50e+03 pdb=" NC PHO D 411 " -0.008 2.00e-02 2.50e+03 pdb=" OBD PHO D 411 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 412 " -0.062 2.00e-02 2.50e+03 9.82e-02 7.71e+02 pdb=" ND PHO D 412 " 0.156 2.00e-02 2.50e+03 pdb=" C1A PHO D 412 " 0.006 2.00e-02 2.50e+03 pdb=" C1B PHO D 412 " -0.041 2.00e-02 2.50e+03 pdb=" C1C PHO D 412 " -0.005 2.00e-02 2.50e+03 pdb=" C1D PHO D 412 " 0.024 2.00e-02 2.50e+03 pdb=" C2A PHO D 412 " 0.240 2.00e-02 2.50e+03 pdb=" C2B PHO D 412 " 0.053 2.00e-02 2.50e+03 pdb=" C2C PHO D 412 " -0.012 2.00e-02 2.50e+03 pdb=" C2D PHO D 412 " 0.005 2.00e-02 2.50e+03 pdb=" C3A PHO D 412 " -0.205 2.00e-02 2.50e+03 pdb=" C3B PHO D 412 " 0.080 2.00e-02 2.50e+03 pdb=" C3C PHO D 412 " -0.038 2.00e-02 2.50e+03 pdb=" C3D PHO D 412 " 0.043 2.00e-02 2.50e+03 pdb=" C4A PHO D 412 " -0.168 2.00e-02 2.50e+03 pdb=" C4B PHO D 412 " 0.008 2.00e-02 2.50e+03 pdb=" C4C PHO D 412 " -0.046 2.00e-02 2.50e+03 pdb=" C4D PHO D 412 " 0.072 2.00e-02 2.50e+03 pdb=" CAB PHO D 412 " 0.160 2.00e-02 2.50e+03 pdb=" CAC PHO D 412 " -0.058 2.00e-02 2.50e+03 pdb=" CAD PHO D 412 " 0.053 2.00e-02 2.50e+03 pdb=" CBD PHO D 412 " -0.073 2.00e-02 2.50e+03 pdb=" CHA PHO D 412 " -0.001 2.00e-02 2.50e+03 pdb=" CHB PHO D 412 " -0.086 2.00e-02 2.50e+03 pdb=" CHC PHO D 412 " 0.008 2.00e-02 2.50e+03 pdb=" CHD PHO D 412 " -0.068 2.00e-02 2.50e+03 pdb=" CMB PHO D 412 " 0.099 2.00e-02 2.50e+03 pdb=" CMC PHO D 412 " 0.003 2.00e-02 2.50e+03 pdb=" CMD PHO D 412 " -0.037 2.00e-02 2.50e+03 pdb=" NA PHO D 412 " -0.224 2.00e-02 2.50e+03 pdb=" NC PHO D 412 " -0.023 2.00e-02 2.50e+03 pdb=" OBD PHO D 412 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA B 609 " -0.081 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" ND CLA B 609 " -0.078 2.00e-02 2.50e+03 pdb=" NA CLA B 609 " -0.070 2.00e-02 2.50e+03 pdb=" NC CLA B 609 " -0.067 2.00e-02 2.50e+03 pdb="MG CLA B 609 " 0.297 2.00e-02 2.50e+03 ... (remaining 3569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 200 2.64 - 3.21: 17734 3.21 - 3.77: 29509 3.77 - 4.34: 41685 4.34 - 4.90: 71220 Nonbonded interactions: 160348 Sorted by model distance: nonbonded pdb=" O ASP D 297 " pdb=" OH TYR D 315 " model vdw 2.080 3.040 nonbonded pdb=" NE2 HIS F 23 " pdb="FE HEM E 101 " model vdw 2.128 3.080 nonbonded pdb=" OH TYR E 19 " pdb=" O THR 1 60 " model vdw 2.184 3.040 nonbonded pdb=" O GLY C 390 " pdb=" ND2 ASN A 298 " model vdw 2.191 3.120 nonbonded pdb=" O ARG B 127 " pdb=" OG1 THR B 128 " model vdw 2.218 3.040 ... (remaining 160343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 55.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.007 0.178 21032 Z= 0.372 Angle : 1.193 18.453 28997 Z= 0.448 Chirality : 0.040 0.221 2809 Planarity : 0.014 0.149 3572 Dihedral : 18.029 135.215 7567 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.55 (0.19), residues: 2063 helix: 2.10 (0.15), residues: 1251 sheet: -0.60 (0.80), residues: 42 loop : -0.69 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 113 HIS 0.006 0.001 HIS B 202 PHE 0.051 0.001 PHE D 185 TYR 0.009 0.001 TYR D 296 ARG 0.009 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.779 Fit side-chains REVERT: B 37 MET cc_start: 0.8157 (mmm) cc_final: 0.7934 (mmt) REVERT: B 175 THR cc_start: 0.8323 (p) cc_final: 0.8085 (p) REVERT: B 256 MET cc_start: 0.8746 (tpp) cc_final: 0.8465 (tpp) REVERT: L 13 LEU cc_start: 0.8690 (tp) cc_final: 0.8470 (tp) outliers start: 0 outliers final: 2 residues processed: 173 average time/residue: 1.0974 time to fit residues: 220.2284 Evaluate side-chains 141 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain A residue 218 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN Z 58 ASN A 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21032 Z= 0.185 Angle : 0.619 12.700 28997 Z= 0.281 Chirality : 0.043 0.334 2809 Planarity : 0.005 0.057 3572 Dihedral : 16.419 122.029 4058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 1.24 % Allowed : 6.82 % Favored : 91.94 % 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: 1.72 (0.19), residues: 2063 helix: 2.21 (0.15), residues: 1268 sheet: -0.10 (0.92), residues: 32 loop : -0.67 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 191 HIS 0.009 0.002 HIS B 201 PHE 0.018 0.001 PHE D 113 TYR 0.010 0.001 TYR L 35 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.916 Fit side-chains REVERT: B 37 MET cc_start: 0.8332 (mmm) cc_final: 0.8066 (tpt) REVERT: B 84 THR cc_start: 0.7834 (t) cc_final: 0.7627 (m) REVERT: B 256 MET cc_start: 0.8793 (tpp) cc_final: 0.8535 (tpp) REVERT: D 220 ASN cc_start: 0.8261 (m110) cc_final: 0.7915 (m-40) REVERT: I 23 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8450 (m-80) REVERT: C 17 GLU cc_start: 0.8186 (pt0) cc_final: 0.7912 (mp0) REVERT: C 372 ILE cc_start: 0.8045 (mt) cc_final: 0.7819 (mp) REVERT: A 331 MET cc_start: 0.8250 (mmm) cc_final: 0.8045 (tpt) outliers start: 21 outliers final: 5 residues processed: 161 average time/residue: 1.1634 time to fit residues: 215.8109 Evaluate side-chains 147 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 0.0770 chunk 200 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 HIS F 40 GLN H 69 ASN V 32 ASN A 76 ASN A 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21032 Z= 0.371 Angle : 0.683 12.851 28997 Z= 0.317 Chirality : 0.046 0.340 2809 Planarity : 0.006 0.057 3572 Dihedral : 16.234 123.129 4054 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 2.24 % Allowed : 10.12 % Favored : 87.65 % 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: 1.31 (0.19), residues: 2063 helix: 1.95 (0.15), residues: 1251 sheet: -0.22 (0.94), residues: 32 loop : -0.89 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 247 HIS 0.008 0.002 HIS C 429 PHE 0.027 0.002 PHE D 113 TYR 0.017 0.002 TYR D 244 ARG 0.007 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.974 Fit side-chains REVERT: B 81 SER cc_start: 0.9051 (p) cc_final: 0.8751 (m) REVERT: B 256 MET cc_start: 0.8819 (tpp) cc_final: 0.8394 (tpp) REVERT: D 24 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: D 220 ASN cc_start: 0.8327 (m110) cc_final: 0.8040 (m-40) REVERT: E 69 ARG cc_start: 0.9036 (ttt180) cc_final: 0.8481 (ttt180) REVERT: I 23 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8658 (m-80) REVERT: C 17 GLU cc_start: 0.8154 (pt0) cc_final: 0.7876 (mp0) REVERT: C 234 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 37 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: A 266 ASN cc_start: 0.7847 (t0) cc_final: 0.7587 (t160) REVERT: A 298 ASN cc_start: 0.7137 (m-40) cc_final: 0.6753 (m-40) REVERT: A 331 MET cc_start: 0.8449 (mmm) cc_final: 0.8198 (tpt) outliers start: 38 outliers final: 19 residues processed: 163 average time/residue: 1.2527 time to fit residues: 233.2702 Evaluate side-chains 168 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 32 ASN A 303 ASN A 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21032 Z= 0.173 Angle : 0.561 11.143 28997 Z= 0.262 Chirality : 0.040 0.325 2809 Planarity : 0.005 0.058 3572 Dihedral : 15.566 120.892 4054 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 1.94 % Allowed : 11.82 % Favored : 86.24 % 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: 1.67 (0.19), residues: 2063 helix: 2.25 (0.15), residues: 1261 sheet: -0.04 (0.94), residues: 32 loop : -0.82 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.005 0.001 HIS B 201 PHE 0.020 0.001 PHE D 113 TYR 0.011 0.001 TYR A 126 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.864 Fit side-chains REVERT: B 81 SER cc_start: 0.9010 (p) cc_final: 0.8732 (m) REVERT: B 256 MET cc_start: 0.8835 (tpp) cc_final: 0.8410 (tpp) REVERT: D 24 GLN cc_start: 0.8465 (mt0) cc_final: 0.8195 (tt0) REVERT: D 220 ASN cc_start: 0.8282 (m110) cc_final: 0.8009 (m-40) REVERT: D 265 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6877 (ttp-170) REVERT: E 69 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8429 (ttt180) REVERT: E 80 SER cc_start: 0.9278 (t) cc_final: 0.8982 (m) REVERT: I 1 MET cc_start: 0.8504 (pmm) cc_final: 0.7981 (pmm) REVERT: I 23 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: C 17 GLU cc_start: 0.8188 (pt0) cc_final: 0.7927 (mp0) REVERT: C 168 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: A 266 ASN cc_start: 0.7721 (t0) cc_final: 0.7433 (t160) REVERT: A 331 MET cc_start: 0.8344 (mmm) cc_final: 0.8078 (tpt) outliers start: 33 outliers final: 13 residues processed: 168 average time/residue: 1.1837 time to fit residues: 229.2659 Evaluate side-chains 164 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 0.0470 chunk 2 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 HIS F 40 GLN V 32 ASN A 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21032 Z= 0.392 Angle : 0.670 12.645 28997 Z= 0.312 Chirality : 0.045 0.338 2809 Planarity : 0.006 0.061 3572 Dihedral : 15.932 121.664 4054 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 2.71 % Allowed : 12.65 % Favored : 84.65 % 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: 1.27 (0.19), residues: 2063 helix: 1.97 (0.15), residues: 1252 sheet: -0.35 (0.95), residues: 32 loop : -1.01 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 247 HIS 0.008 0.002 HIS C 429 PHE 0.029 0.002 PHE D 113 TYR 0.015 0.002 TYR D 244 ARG 0.006 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 156 time to evaluate : 1.837 Fit side-chains REVERT: B 81 SER cc_start: 0.8994 (p) cc_final: 0.8788 (m) REVERT: B 256 MET cc_start: 0.8845 (tpp) cc_final: 0.8417 (tpp) REVERT: D 14 TRP cc_start: 0.8010 (t60) cc_final: 0.7778 (t60) REVERT: D 24 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: D 220 ASN cc_start: 0.8278 (m110) cc_final: 0.8015 (m-40) REVERT: D 265 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6856 (ttp-170) REVERT: D 271 MET cc_start: 0.8562 (mtt) cc_final: 0.8262 (mtt) REVERT: E 69 ARG cc_start: 0.9060 (ttt180) cc_final: 0.8551 (ttt180) REVERT: E 80 SER cc_start: 0.9285 (t) cc_final: 0.8996 (m) REVERT: I 23 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8611 (m-80) REVERT: C 17 GLU cc_start: 0.8079 (pt0) cc_final: 0.7829 (mp0) REVERT: C 72 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: A 37 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7765 (ptm) REVERT: A 64 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6405 (mtm-85) REVERT: A 266 ASN cc_start: 0.7786 (t0) cc_final: 0.7514 (t160) REVERT: A 331 MET cc_start: 0.8431 (mmm) cc_final: 0.8202 (tpt) outliers start: 46 outliers final: 24 residues processed: 178 average time/residue: 1.1970 time to fit residues: 244.0691 Evaluate side-chains 178 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.5980 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 197 optimal weight: 0.4980 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21032 Z= 0.161 Angle : 0.538 9.606 28997 Z= 0.254 Chirality : 0.039 0.311 2809 Planarity : 0.004 0.061 3572 Dihedral : 15.060 119.998 4054 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.76 % Allowed : 14.41 % Favored : 83.82 % 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: 1.74 (0.19), residues: 2063 helix: 2.35 (0.15), residues: 1256 sheet: -0.11 (0.94), residues: 32 loop : -0.85 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 21 HIS 0.005 0.001 HIS B 201 PHE 0.015 0.001 PHE D 113 TYR 0.012 0.001 TYR A 107 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 2.043 Fit side-chains REVERT: B 256 MET cc_start: 0.8846 (tpp) cc_final: 0.8481 (tpp) REVERT: D 14 TRP cc_start: 0.7771 (t60) cc_final: 0.7504 (t60) REVERT: D 220 ASN cc_start: 0.8259 (m110) cc_final: 0.8011 (m-40) REVERT: D 265 ARG cc_start: 0.6890 (ttt-90) cc_final: 0.6453 (ttp-170) REVERT: E 69 ARG cc_start: 0.8993 (ttt180) cc_final: 0.8568 (ttt180) REVERT: I 23 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: C 17 GLU cc_start: 0.8117 (pt0) cc_final: 0.7898 (mp0) REVERT: C 168 MET cc_start: 0.8639 (ttp) cc_final: 0.8084 (mtp) REVERT: C 273 ILE cc_start: 0.8261 (mt) cc_final: 0.7985 (mp) REVERT: A 37 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7525 (ptm) REVERT: A 266 ASN cc_start: 0.7640 (t0) cc_final: 0.7358 (t160) REVERT: A 331 MET cc_start: 0.8300 (mmm) cc_final: 0.8092 (tpt) outliers start: 30 outliers final: 15 residues processed: 174 average time/residue: 1.1749 time to fit residues: 235.3881 Evaluate side-chains 168 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN V 32 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21032 Z= 0.308 Angle : 0.611 12.391 28997 Z= 0.287 Chirality : 0.042 0.319 2809 Planarity : 0.005 0.061 3572 Dihedral : 15.241 121.027 4054 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 2.18 % Allowed : 14.94 % Favored : 82.88 % 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: 1.52 (0.19), residues: 2063 helix: 2.18 (0.15), residues: 1258 sheet: -0.22 (0.94), residues: 32 loop : -0.96 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 247 HIS 0.007 0.001 HIS C 429 PHE 0.028 0.002 PHE D 113 TYR 0.012 0.002 TYR A 126 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.732 Fit side-chains REVERT: B 256 MET cc_start: 0.8863 (tpp) cc_final: 0.8506 (tpp) REVERT: B 422 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8257 (ttm110) REVERT: D 14 TRP cc_start: 0.7928 (t60) cc_final: 0.7693 (t60) REVERT: D 220 ASN cc_start: 0.8270 (m110) cc_final: 0.8011 (m-40) REVERT: D 265 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6754 (ttp-170) REVERT: E 69 ARG cc_start: 0.9036 (ttt180) cc_final: 0.8505 (ttt180) REVERT: I 23 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: C 17 GLU cc_start: 0.8126 (pt0) cc_final: 0.7885 (mp0) REVERT: C 168 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: A 37 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7722 (ptm) REVERT: A 266 ASN cc_start: 0.7718 (t0) cc_final: 0.7474 (t160) REVERT: A 331 MET cc_start: 0.8402 (mmm) cc_final: 0.8187 (tpt) outliers start: 37 outliers final: 20 residues processed: 174 average time/residue: 1.2428 time to fit residues: 248.4811 Evaluate side-chains 177 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 178 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21032 Z= 0.174 Angle : 0.543 10.451 28997 Z= 0.258 Chirality : 0.040 0.308 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.911 120.230 4054 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.91 % Favored : 97.04 % Rotamer: Outliers : 1.94 % Allowed : 15.18 % Favored : 82.88 % 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: 1.72 (0.19), residues: 2063 helix: 2.34 (0.15), residues: 1258 sheet: -0.00 (0.93), residues: 32 loop : -0.91 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.004 0.001 HIS C 429 PHE 0.020 0.001 PHE D 113 TYR 0.010 0.001 TYR A 126 ARG 0.007 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.986 Fit side-chains REVERT: B 256 MET cc_start: 0.8858 (tpp) cc_final: 0.8497 (tpp) REVERT: B 422 ARG cc_start: 0.8462 (ttm110) cc_final: 0.8235 (ttm110) REVERT: B 467 ILE cc_start: 0.7766 (mm) cc_final: 0.7558 (mp) REVERT: D 14 TRP cc_start: 0.7836 (t60) cc_final: 0.7568 (t60) REVERT: D 220 ASN cc_start: 0.8255 (m110) cc_final: 0.7998 (m-40) REVERT: D 265 ARG cc_start: 0.7105 (ttt-90) cc_final: 0.6659 (ttp-170) REVERT: E 69 ARG cc_start: 0.8995 (ttt180) cc_final: 0.8530 (ttt180) REVERT: I 23 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: C 17 GLU cc_start: 0.8140 (pt0) cc_final: 0.7902 (mp0) REVERT: C 168 MET cc_start: 0.8628 (ttp) cc_final: 0.8091 (mtp) REVERT: A 37 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7551 (ptm) REVERT: A 266 ASN cc_start: 0.7646 (t0) cc_final: 0.7363 (t160) outliers start: 33 outliers final: 22 residues processed: 173 average time/residue: 1.1725 time to fit residues: 233.5955 Evaluate side-chains 177 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN V 32 ASN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21032 Z= 0.200 Angle : 0.562 11.568 28997 Z= 0.265 Chirality : 0.041 0.314 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.864 120.230 4054 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.66 % Rotamer: Outliers : 1.76 % Allowed : 15.24 % Favored : 83.00 % 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: 1.72 (0.19), residues: 2063 helix: 2.34 (0.15), residues: 1258 sheet: 0.07 (0.94), residues: 32 loop : -0.90 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 21 HIS 0.005 0.001 HIS C 429 PHE 0.023 0.001 PHE D 113 TYR 0.009 0.001 TYR A 126 ARG 0.009 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.987 Fit side-chains REVERT: B 256 MET cc_start: 0.8854 (tpp) cc_final: 0.8488 (tpp) REVERT: B 422 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8218 (ttm110) REVERT: D 14 TRP cc_start: 0.7864 (t60) cc_final: 0.7640 (t60) REVERT: D 126 MET cc_start: 0.8427 (ttt) cc_final: 0.8199 (ttt) REVERT: D 220 ASN cc_start: 0.8253 (m110) cc_final: 0.8003 (m-40) REVERT: D 265 ARG cc_start: 0.7123 (ttt-90) cc_final: 0.6666 (ttp-170) REVERT: E 69 ARG cc_start: 0.8998 (ttt180) cc_final: 0.8532 (ttt180) REVERT: I 23 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: C 17 GLU cc_start: 0.8142 (pt0) cc_final: 0.7900 (mp0) REVERT: C 168 MET cc_start: 0.8634 (ttp) cc_final: 0.8089 (mtp) REVERT: A 37 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7572 (ptm) REVERT: A 266 ASN cc_start: 0.7646 (t0) cc_final: 0.7359 (t160) outliers start: 30 outliers final: 21 residues processed: 171 average time/residue: 1.1836 time to fit residues: 233.1447 Evaluate side-chains 176 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 32 ASN C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21032 Z= 0.213 Angle : 0.563 10.872 28997 Z= 0.268 Chirality : 0.041 0.305 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.838 120.268 4054 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.71 % Allowed : 15.53 % Favored : 82.76 % 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: 1.68 (0.19), residues: 2063 helix: 2.29 (0.15), residues: 1259 sheet: 0.17 (0.95), residues: 32 loop : -0.89 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 21 HIS 0.005 0.001 HIS C 429 PHE 0.025 0.001 PHE D 113 TYR 0.010 0.001 TYR A 126 ARG 0.008 0.000 ARG C 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.877 Fit side-chains REVERT: B 256 MET cc_start: 0.8866 (tpp) cc_final: 0.8505 (tpp) REVERT: D 14 TRP cc_start: 0.7878 (t60) cc_final: 0.7619 (t60) REVERT: D 220 ASN cc_start: 0.8251 (m110) cc_final: 0.7998 (m-40) REVERT: D 265 ARG cc_start: 0.7123 (ttt-90) cc_final: 0.6665 (ttp-170) REVERT: E 69 ARG cc_start: 0.9016 (ttt180) cc_final: 0.8477 (ttt180) REVERT: I 23 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: C 17 GLU cc_start: 0.8127 (pt0) cc_final: 0.7892 (mp0) REVERT: C 168 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8133 (mtp) REVERT: A 64 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7800 (mmt-90) REVERT: A 266 ASN cc_start: 0.7661 (t0) cc_final: 0.7390 (t160) outliers start: 29 outliers final: 22 residues processed: 176 average time/residue: 1.1922 time to fit residues: 241.1097 Evaluate side-chains 180 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain 1 residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN V 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.092631 restraints weight = 29753.209| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.80 r_work: 0.3111 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21032 Z= 0.253 Angle : 0.577 11.840 28997 Z= 0.274 Chirality : 0.042 0.311 2809 Planarity : 0.005 0.061 3572 Dihedral : 14.920 120.645 4054 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.65 % Allowed : 15.59 % Favored : 82.76 % 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: 1.60 (0.19), residues: 2063 helix: 2.24 (0.15), residues: 1252 sheet: 0.17 (0.97), residues: 32 loop : -0.93 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 21 HIS 0.006 0.001 HIS C 429 PHE 0.026 0.001 PHE D 113 TYR 0.011 0.001 TYR A 126 ARG 0.007 0.000 ARG C 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5030.65 seconds wall clock time: 89 minutes 57.12 seconds (5397.12 seconds total)