Starting phenix.real_space_refine on Sun Oct 12 06:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kde_37133/10_2025/8kde_37133.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.995 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 10 5.49 5 Mg 35 5.21 5 S 69 5.16 5 C 15202 2.51 5 N 3158 2.21 5 O 3611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22087 Number of models: 1 Model: "" Number of chains: 28 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: "G" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1070 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "3" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 694 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 320 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 1379 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 3, 'LMG': 2} Classifications: {'undetermined': 24} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 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: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 600 Unusual residues: {'BCR': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 2, 'PL9': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'LHG': 1, 'VTQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 1196 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'FE2': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.27 Number of scatterers: 22087 At special positions: 0 Unit cell: (113.36, 158.08, 127.92, 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 69 16.00 P 10 15.00 Mg 35 11.99 O 3611 8.00 N 3158 7.00 C 15202 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 - 3.00 Amino acid : True - 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: 2.52 Conformation dependent library (CDL) restraints added in 994.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 8 sheets defined 68.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.838A pdb=" N GLY B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 68 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 Processing helix chain 'B' and resid 195 through 219 removed outlier: 3.835A pdb=" N ALA B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.649A 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 233 through 259 removed outlier: 4.431A pdb=" N VAL B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.762A 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 330 through 335 removed outlier: 3.622A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) 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 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: 4.064A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.100A 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 57 through 62 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 136 removed outlier: 4.053A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 3.877A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Proline residue: D 149 - end of helix removed outlier: 4.282A 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 190 Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 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: 3.875A 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: 4.495A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (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 16 removed outlier: 3.848A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 removed outlier: 3.998A pdb=" N TRP E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.625A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 41 removed outlier: 3.784A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix removed outlier: 3.808A 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 Processing helix chain 'H' and resid 46 through 69 Processing helix chain 'H' and resid 80 through 85 Processing helix chain 'I' and resid 2 through 24 Processing helix chain 'I' and resid 26 through 30 removed outlier: 3.505A pdb=" N ALA I 29 " --> pdb=" O ASN I 26 " (cutoff:3.500A) 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: 3.687A pdb=" N VAL K 22 " --> pdb=" O PHE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 27 through 42 removed outlier: 3.654A pdb=" N PHE K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.614A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.767A 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 Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 3 through 29 removed outlier: 3.893A pdb=" N GLY V 19 " --> pdb=" O VAL V 15 " (cutoff:3.500A) Proline residue: V 20 - end of helix removed outlier: 3.771A 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 'G' and resid 60 through 67 removed outlier: 3.626A pdb=" N ASN G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 87 removed outlier: 3.518A pdb=" N ARG G 71 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG G 76 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL G 78 " --> pdb=" O GLN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 116 removed outlier: 4.102A pdb=" N SER G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 127 removed outlier: 3.715A pdb=" N SER G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 145 through 164 removed outlier: 3.606A pdb=" N LYS G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 188 Processing helix chain 'G' and resid 189 through 194 removed outlier: 4.362A pdb=" N LYS G 194 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 105 removed outlier: 3.643A pdb=" N ALA 3 70 " --> pdb=" O PRO 3 66 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY 3 81 " --> pdb=" O GLY 3 77 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL 3 84 " --> pdb=" O GLN 3 80 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU 3 85 " --> pdb=" O GLY 3 81 " (cutoff:3.500A) Processing helix chain '3' and resid 120 through 128 removed outlier: 3.726A pdb=" N SER 3 124 " --> pdb=" O LEU 3 120 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA 3 128 " --> pdb=" O SER 3 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 5.942A 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 72 Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.685A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.703A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 removed outlier: 3.689A 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: 3.990A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 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 341 through 347 removed outlier: 4.166A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.799A pdb=" N THR C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'C' and resid 452 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 95 through 99 Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.946A 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 142 through 166 removed outlier: 3.901A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.974A 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 Processing helix chain 'A' and resid 175 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 250 through 259 removed outlier: 4.150A pdb=" N TYR A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 removed outlier: 3.738A pdb=" N HIS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 308 through 312 removed outlier: 4.276A pdb=" N ARG A 312 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 Processing helix chain '1' and resid 31 through 63 removed outlier: 3.690A pdb=" N MET 1 35 " --> pdb=" O THR 1 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 1 39 " --> pdb=" O MET 1 35 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA 1 46 " --> pdb=" O ALA 1 42 " (cutoff:3.500A) Proline residue: 1 51 - end of helix Proline residue: 1 58 - end of helix 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: 7.093A 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 377 through 380 removed outlier: 6.817A pdb=" N LEU B 370 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.817A pdb=" N LEU B 370 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N TRP B 340 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE B 429 " --> pdb=" O TRP B 340 " (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 '3' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA8, first strand: chain 'C' and resid 329 through 331 1124 hydrogen bonds defined for protein. 3216 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: 4.05 Time building geometry restraints manager: 3.19 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: 6454 1.37 - 1.55: 16122 1.55 - 1.73: 74 1.73 - 1.92: 119 1.92 - 2.10: 144 Bond restraints: 22913 Sorted by residual: bond pdb=" C6 SQD C 620 " pdb=" S SQD C 620 " ideal model delta sigma weight residual 1.840 1.668 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" C7 LHG B 621 " pdb=" O7 LHG B 621 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C7 LHG K 103 " pdb=" O7 LHG K 103 " ideal model delta sigma weight residual 1.329 1.457 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C7 LHG A 408 " pdb=" O7 LHG A 408 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C7 LHG D 405 " pdb=" O7 LHG D 405 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 ... (remaining 22908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 30883 3.65 - 7.31: 495 7.31 - 10.96: 65 10.96 - 14.62: 31 14.62 - 18.27: 32 Bond angle restraints: 31506 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 176.90 158.63 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" NB CLA B 604 " pdb="MG CLA B 604 " pdb=" ND CLA B 604 " ideal model delta sigma weight residual 176.90 158.75 18.15 3.00e+00 1.11e-01 3.66e+01 angle pdb=" NB CLA C 604 " pdb="MG CLA C 604 " pdb=" ND CLA C 604 " ideal model delta sigma weight residual 176.90 159.18 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" NB CLA B 611 " pdb="MG CLA B 611 " pdb=" ND CLA B 611 " ideal model delta sigma weight residual 176.90 159.21 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" NB CLA C 606 " pdb="MG CLA C 606 " pdb=" ND CLA C 606 " ideal model delta sigma weight residual 176.90 159.69 17.21 3.00e+00 1.11e-01 3.29e+01 ... (remaining 31501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.27: 11770 27.27 - 54.53: 635 54.53 - 81.80: 86 81.80 - 109.06: 23 109.06 - 136.33: 24 Dihedral angle restraints: 12538 sinusoidal: 5921 harmonic: 6617 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 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA TYR D 296 " pdb=" C TYR D 296 " pdb=" N ASP D 297 " pdb=" CA ASP D 297 " ideal model delta harmonic sigma weight residual 180.00 -157.30 -22.70 0 5.00e+00 4.00e-02 2.06e+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 -24.22 112.11 -136.33 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 12535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2521 0.051 - 0.102: 495 0.102 - 0.154: 62 0.154 - 0.205: 11 0.205 - 0.256: 6 Chirality restraints: 3095 Sorted by residual: chirality pdb=" C2 LHG B 622 " pdb=" C1 LHG B 622 " pdb=" C3 LHG B 622 " pdb=" O2 LHG B 622 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.26 2.00e-01 2.50e+01 1.64e+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 -2.55 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 1.20e+00 ... (remaining 3092 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO D 410 " 0.113 2.00e-02 2.50e+03 1.15e-01 1.05e+03 pdb=" ND PHO D 410 " 0.073 2.00e-02 2.50e+03 pdb=" C1A PHO D 410 " -0.020 2.00e-02 2.50e+03 pdb=" C1B PHO D 410 " 0.058 2.00e-02 2.50e+03 pdb=" C1C PHO D 410 " 0.018 2.00e-02 2.50e+03 pdb=" C1D PHO D 410 " 0.015 2.00e-02 2.50e+03 pdb=" C2A PHO D 410 " -0.151 2.00e-02 2.50e+03 pdb=" C2B PHO D 410 " -0.099 2.00e-02 2.50e+03 pdb=" C2C PHO D 410 " 0.042 2.00e-02 2.50e+03 pdb=" C2D PHO D 410 " -0.021 2.00e-02 2.50e+03 pdb=" C3A PHO D 410 " 0.302 2.00e-02 2.50e+03 pdb=" C3B PHO D 410 " -0.129 2.00e-02 2.50e+03 pdb=" C3C PHO D 410 " 0.040 2.00e-02 2.50e+03 pdb=" C3D PHO D 410 " -0.050 2.00e-02 2.50e+03 pdb=" C4A PHO D 410 " 0.205 2.00e-02 2.50e+03 pdb=" C4B PHO D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C4C PHO D 410 " 0.008 2.00e-02 2.50e+03 pdb=" C4D PHO D 410 " -0.013 2.00e-02 2.50e+03 pdb=" CAB PHO D 410 " -0.259 2.00e-02 2.50e+03 pdb=" CAC PHO D 410 " 0.061 2.00e-02 2.50e+03 pdb=" CAD PHO D 410 " -0.087 2.00e-02 2.50e+03 pdb=" CBD PHO D 410 " -0.147 2.00e-02 2.50e+03 pdb=" CHA PHO D 410 " -0.060 2.00e-02 2.50e+03 pdb=" CHB PHO D 410 " 0.137 2.00e-02 2.50e+03 pdb=" CHC PHO D 410 " 0.023 2.00e-02 2.50e+03 pdb=" CHD PHO D 410 " -0.016 2.00e-02 2.50e+03 pdb=" CMB PHO D 410 " -0.191 2.00e-02 2.50e+03 pdb=" CMC PHO D 410 " 0.070 2.00e-02 2.50e+03 pdb=" CMD PHO D 410 " -0.040 2.00e-02 2.50e+03 pdb=" NA PHO D 410 " 0.192 2.00e-02 2.50e+03 pdb=" NC PHO D 410 " -0.005 2.00e-02 2.50e+03 pdb=" OBD PHO D 410 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 411 " -0.092 2.00e-02 2.50e+03 1.12e-01 1.00e+03 pdb=" ND PHO D 411 " 0.068 2.00e-02 2.50e+03 pdb=" C1A PHO D 411 " 0.002 2.00e-02 2.50e+03 pdb=" C1B PHO D 411 " -0.050 2.00e-02 2.50e+03 pdb=" C1C PHO D 411 " 0.013 2.00e-02 2.50e+03 pdb=" C1D PHO D 411 " 0.020 2.00e-02 2.50e+03 pdb=" C2A PHO D 411 " 0.217 2.00e-02 2.50e+03 pdb=" C2B PHO D 411 " 0.081 2.00e-02 2.50e+03 pdb=" C2C PHO D 411 " -0.028 2.00e-02 2.50e+03 pdb=" C2D PHO D 411 " 0.024 2.00e-02 2.50e+03 pdb=" C3A PHO D 411 " -0.281 2.00e-02 2.50e+03 pdb=" C3B PHO D 411 " 0.112 2.00e-02 2.50e+03 pdb=" C3C PHO D 411 " -0.060 2.00e-02 2.50e+03 pdb=" C3D PHO D 411 " 0.058 2.00e-02 2.50e+03 pdb=" C4A PHO D 411 " -0.213 2.00e-02 2.50e+03 pdb=" C4B PHO D 411 " 0.003 2.00e-02 2.50e+03 pdb=" C4C PHO D 411 " -0.017 2.00e-02 2.50e+03 pdb=" C4D PHO D 411 " 0.058 2.00e-02 2.50e+03 pdb=" CAB PHO D 411 " 0.226 2.00e-02 2.50e+03 pdb=" CAC PHO D 411 " -0.115 2.00e-02 2.50e+03 pdb=" CAD PHO D 411 " 0.072 2.00e-02 2.50e+03 pdb=" CBD PHO D 411 " 0.025 2.00e-02 2.50e+03 pdb=" CHA PHO D 411 " 0.022 2.00e-02 2.50e+03 pdb=" CHB PHO D 411 " -0.117 2.00e-02 2.50e+03 pdb=" CHC PHO D 411 " -0.009 2.00e-02 2.50e+03 pdb=" CHD PHO D 411 " -0.016 2.00e-02 2.50e+03 pdb=" CMB PHO D 411 " 0.151 2.00e-02 2.50e+03 pdb=" CMC PHO D 411 " -0.054 2.00e-02 2.50e+03 pdb=" CMD PHO D 411 " -0.001 2.00e-02 2.50e+03 pdb=" NA PHO D 411 " -0.244 2.00e-02 2.50e+03 pdb=" NC PHO D 411 " 0.036 2.00e-02 2.50e+03 pdb=" OBD PHO D 411 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CLA B 604 " 0.079 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" ND CLA B 604 " 0.077 2.00e-02 2.50e+03 pdb=" NA CLA B 604 " 0.070 2.00e-02 2.50e+03 pdb=" NC CLA B 604 " 0.067 2.00e-02 2.50e+03 pdb="MG CLA B 604 " -0.293 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 285 2.64 - 3.20: 19812 3.20 - 3.77: 33710 3.77 - 4.33: 48500 4.33 - 4.90: 81565 Nonbonded interactions: 183872 Sorted by model distance: nonbonded pdb=" O ASP D 297 " pdb=" OH TYR D 315 " model vdw 2.069 3.040 nonbonded pdb=" O1 LHG D 407 " pdb=" O3 LHG D 407 " model vdw 2.083 3.040 nonbonded pdb=" O SER 3 64 " pdb=" OG SER 3 65 " model vdw 2.095 3.040 nonbonded pdb=" OG SER B 222 " pdb=" O GLY H 43 " model vdw 2.100 3.040 nonbonded pdb=" NH2 ARG C 185 " pdb=" OE2 GLU C 219 " model vdw 2.131 3.120 ... (remaining 183867 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: 2.880 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.730 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.172 22942 Z= 0.441 Angle : 1.177 18.273 31506 Z= 0.435 Chirality : 0.042 0.256 3095 Planarity : 0.013 0.147 3888 Dihedral : 17.452 136.325 8312 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.18), residues: 2302 helix: 1.97 (0.14), residues: 1418 sheet: -1.30 (0.76), residues: 47 loop : -0.65 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.011 0.001 TYR A 126 PHE 0.032 0.001 PHE B 250 TRP 0.011 0.001 TRP B 247 HIS 0.008 0.001 HIS 1 60 Details of bonding type rmsd covalent geometry : bond 0.00736 (22913) covalent geometry : angle 1.17739 (31506) hydrogen bonds : bond 0.12723 ( 1120) hydrogen bonds : angle 5.95484 ( 3216) Misc. bond : bond 0.07535 ( 29) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: F 39 MET cc_start: 0.8827 (mtt) cc_final: 0.8486 (mtt) REVERT: H 69 ASN cc_start: 0.8752 (t0) cc_final: 0.8524 (t0) REVERT: G 106 LYS cc_start: 0.7101 (ttmm) cc_final: 0.6573 (ttmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.7839 time to fit residues: 160.6660 Evaluate side-chains 139 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN A 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086911 restraints weight = 33307.086| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.70 r_work: 0.3137 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 22942 Z= 0.156 Angle : 0.633 15.210 31506 Z= 0.288 Chirality : 0.042 0.358 3095 Planarity : 0.005 0.044 3888 Dihedral : 16.941 122.051 4403 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 1.11 % Allowed : 5.89 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.18), residues: 2302 helix: 2.04 (0.14), residues: 1438 sheet: -0.75 (0.84), residues: 37 loop : -0.66 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 472 TYR 0.021 0.001 TYR H 68 PHE 0.013 0.001 PHE A 295 TRP 0.011 0.001 TRP D 167 HIS 0.006 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00343 (22913) covalent geometry : angle 0.63256 (31506) hydrogen bonds : bond 0.04850 ( 1120) hydrogen bonds : angle 4.74454 ( 3216) Misc. bond : bond 0.04900 ( 29) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.830 Fit side-chains REVERT: B 256 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8650 (tpp) REVERT: D 301 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8260 (tp40) REVERT: F 39 MET cc_start: 0.8990 (mtt) cc_final: 0.8658 (mtt) REVERT: G 93 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7042 (mt) REVERT: C 444 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7536 (pm20) outliers start: 21 outliers final: 4 residues processed: 161 average time/residue: 0.7063 time to fit residues: 129.2139 Evaluate side-chains 148 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 444 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 165 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 223 optimal weight: 0.4980 chunk 216 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086501 restraints weight = 33349.814| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.70 r_work: 0.3134 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 22942 Z= 0.161 Angle : 0.592 12.408 31506 Z= 0.270 Chirality : 0.042 0.331 3095 Planarity : 0.005 0.041 3888 Dihedral : 15.622 120.909 4403 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 1.49 % Allowed : 7.70 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2302 helix: 2.07 (0.14), residues: 1435 sheet: -0.59 (0.86), residues: 37 loop : -0.68 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 472 TYR 0.019 0.001 TYR H 68 PHE 0.014 0.001 PHE A 295 TRP 0.013 0.001 TRP B 247 HIS 0.006 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00374 (22913) covalent geometry : angle 0.59246 (31506) hydrogen bonds : bond 0.04624 ( 1120) hydrogen bonds : angle 4.53558 ( 3216) Misc. bond : bond 0.03983 ( 29) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.754 Fit side-chains REVERT: B 256 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8665 (tpp) REVERT: B 390 TYR cc_start: 0.7638 (m-80) cc_final: 0.7410 (m-80) REVERT: D 301 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8239 (tp40) REVERT: D 307 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7522 (mt-10) REVERT: F 39 MET cc_start: 0.8993 (mtt) cc_final: 0.8666 (mtt) REVERT: H 69 ASN cc_start: 0.9014 (t0) cc_final: 0.8619 (t0) REVERT: G 93 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7162 (mt) REVERT: C 187 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8555 (mm) REVERT: C 189 ASN cc_start: 0.9026 (p0) cc_final: 0.8697 (p0) REVERT: C 311 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7230 (ttm170) outliers start: 28 outliers final: 6 residues processed: 167 average time/residue: 0.7198 time to fit residues: 136.7071 Evaluate side-chains 152 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 364 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 201 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** F 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085070 restraints weight = 33515.809| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.70 r_work: 0.3111 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.227 22942 Z= 0.205 Angle : 0.605 11.690 31506 Z= 0.278 Chirality : 0.043 0.313 3095 Planarity : 0.005 0.043 3888 Dihedral : 15.567 121.467 4403 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 8.49 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.18), residues: 2302 helix: 1.98 (0.14), residues: 1437 sheet: -0.50 (0.88), residues: 37 loop : -0.72 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 472 TYR 0.023 0.001 TYR H 68 PHE 0.016 0.001 PHE B 246 TRP 0.014 0.001 TRP B 247 HIS 0.007 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00488 (22913) covalent geometry : angle 0.60477 (31506) hydrogen bonds : bond 0.04829 ( 1120) hydrogen bonds : angle 4.52427 ( 3216) Misc. bond : bond 0.04401 ( 29) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.707 Fit side-chains REVERT: D 301 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8271 (tp40) REVERT: D 307 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7543 (mt-10) REVERT: F 39 MET cc_start: 0.9024 (mtt) cc_final: 0.8686 (mtt) REVERT: H 69 ASN cc_start: 0.9014 (t0) cc_final: 0.8789 (t0) REVERT: I 23 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: 3 116 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6419 (tp40) REVERT: C 187 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8656 (mm) REVERT: C 189 ASN cc_start: 0.9033 (p0) cc_final: 0.8694 (p0) outliers start: 31 outliers final: 13 residues processed: 166 average time/residue: 0.6970 time to fit residues: 132.2832 Evaluate side-chains 157 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 213 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 20 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 HIS H 34 ASN 3 80 GLN C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086697 restraints weight = 33360.831| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.70 r_work: 0.3141 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.185 22942 Z= 0.125 Angle : 0.546 11.031 31506 Z= 0.253 Chirality : 0.040 0.269 3095 Planarity : 0.004 0.043 3888 Dihedral : 15.245 120.471 4403 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 1.91 % Allowed : 9.34 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2302 helix: 2.14 (0.14), residues: 1438 sheet: -0.50 (0.86), residues: 37 loop : -0.63 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 472 TYR 0.014 0.001 TYR H 68 PHE 0.012 0.001 PHE D 113 TRP 0.012 0.001 TRP D 167 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd covalent geometry : bond 0.00277 (22913) covalent geometry : angle 0.54585 (31506) hydrogen bonds : bond 0.04220 ( 1120) hydrogen bonds : angle 4.34444 ( 3216) Misc. bond : bond 0.03442 ( 29) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.625 Fit side-chains REVERT: D 301 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8215 (tp40) REVERT: D 307 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7501 (mt-10) REVERT: F 39 MET cc_start: 0.8972 (mtt) cc_final: 0.8639 (mtt) REVERT: H 69 ASN cc_start: 0.8982 (t0) cc_final: 0.8719 (t0) REVERT: 3 116 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6389 (tp40) REVERT: C 189 ASN cc_start: 0.9029 (p0) cc_final: 0.8700 (p0) outliers start: 36 outliers final: 16 residues processed: 188 average time/residue: 0.6601 time to fit residues: 142.7551 Evaluate side-chains 175 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 214 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 301 GLN H 34 ASN C 62 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088291 restraints weight = 33470.223| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.71 r_work: 0.3170 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.171 22942 Z= 0.107 Angle : 0.531 10.568 31506 Z= 0.247 Chirality : 0.039 0.239 3095 Planarity : 0.004 0.043 3888 Dihedral : 14.875 119.636 4403 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 10.93 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.18), residues: 2302 helix: 2.27 (0.14), residues: 1432 sheet: -0.50 (0.86), residues: 37 loop : -0.58 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 23 TYR 0.012 0.001 TYR K 15 PHE 0.012 0.001 PHE B 139 TRP 0.014 0.001 TRP D 14 HIS 0.004 0.001 HIS F 23 Details of bonding type rmsd covalent geometry : bond 0.00225 (22913) covalent geometry : angle 0.53114 (31506) hydrogen bonds : bond 0.03860 ( 1120) hydrogen bonds : angle 4.19377 ( 3216) Misc. bond : bond 0.03212 ( 29) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.682 Fit side-chains REVERT: D 307 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7497 (mt-10) REVERT: F 39 MET cc_start: 0.8912 (mtt) cc_final: 0.8580 (mtp) REVERT: H 69 ASN cc_start: 0.8950 (t0) cc_final: 0.8743 (t0) REVERT: 3 116 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.5899 (tp-100) REVERT: C 189 ASN cc_start: 0.9019 (p0) cc_final: 0.8711 (p0) REVERT: C 408 VAL cc_start: 0.8239 (t) cc_final: 0.7968 (m) outliers start: 27 outliers final: 15 residues processed: 194 average time/residue: 0.6531 time to fit residues: 145.6074 Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN H 34 ASN H 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085790 restraints weight = 33424.000| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.71 r_work: 0.3128 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 22942 Z= 0.176 Angle : 0.583 11.028 31506 Z= 0.273 Chirality : 0.042 0.310 3095 Planarity : 0.005 0.060 3888 Dihedral : 15.016 120.651 4403 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 1.49 % Allowed : 11.68 % Favored : 86.84 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.18), residues: 2302 helix: 2.17 (0.14), residues: 1432 sheet: -0.54 (0.86), residues: 37 loop : -0.61 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 23 TYR 0.016 0.001 TYR H 68 PHE 0.020 0.001 PHE B 246 TRP 0.016 0.001 TRP D 14 HIS 0.051 0.002 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00410 (22913) covalent geometry : angle 0.58302 (31506) hydrogen bonds : bond 0.04391 ( 1120) hydrogen bonds : angle 4.29958 ( 3216) Misc. bond : bond 0.03891 ( 29) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.756 Fit side-chains REVERT: D 307 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7493 (mt-10) REVERT: F 39 MET cc_start: 0.8993 (mtt) cc_final: 0.8664 (mtt) REVERT: G 93 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7247 (mt) REVERT: 3 116 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.5994 (tp-100) REVERT: C 189 ASN cc_start: 0.9019 (p0) cc_final: 0.8722 (p0) REVERT: C 408 VAL cc_start: 0.8353 (t) cc_final: 0.8065 (m) outliers start: 28 outliers final: 16 residues processed: 174 average time/residue: 0.6825 time to fit residues: 135.7666 Evaluate side-chains 178 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 190 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN E 61 GLN H 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085688 restraints weight = 33372.953| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.72 r_work: 0.3128 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 22942 Z= 0.159 Angle : 0.567 10.964 31506 Z= 0.264 Chirality : 0.041 0.250 3095 Planarity : 0.004 0.044 3888 Dihedral : 15.014 120.673 4403 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.31 % Rotamer: Outliers : 1.70 % Allowed : 11.52 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.18), residues: 2302 helix: 2.12 (0.14), residues: 1446 sheet: -0.60 (0.85), residues: 37 loop : -0.64 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 23 TYR 0.012 0.001 TYR H 68 PHE 0.014 0.001 PHE B 246 TRP 0.018 0.001 TRP D 14 HIS 0.007 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00370 (22913) covalent geometry : angle 0.56737 (31506) hydrogen bonds : bond 0.04348 ( 1120) hydrogen bonds : angle 4.28855 ( 3216) Misc. bond : bond 0.03810 ( 29) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.778 Fit side-chains REVERT: D 307 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7512 (mt-10) REVERT: F 39 MET cc_start: 0.8993 (mtt) cc_final: 0.8666 (mtt) REVERT: H 69 ASN cc_start: 0.8945 (t0) cc_final: 0.8595 (t0) REVERT: 3 116 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6036 (tp40) REVERT: C 189 ASN cc_start: 0.9016 (p0) cc_final: 0.8736 (p0) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.6293 time to fit residues: 137.0508 Evaluate side-chains 184 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain T residue 29 MET Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 89 optimal weight: 0.3980 chunk 150 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN E 61 GLN H 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.086608 restraints weight = 33496.566| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.72 r_work: 0.3143 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.187 22942 Z= 0.128 Angle : 0.553 12.826 31506 Z= 0.257 Chirality : 0.040 0.287 3095 Planarity : 0.004 0.044 3888 Dihedral : 14.860 120.012 4403 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 1.38 % Allowed : 12.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.18), residues: 2302 helix: 2.18 (0.14), residues: 1446 sheet: -0.65 (0.84), residues: 37 loop : -0.61 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 23 TYR 0.012 0.001 TYR H 68 PHE 0.012 0.001 PHE I 19 TRP 0.024 0.001 TRP D 14 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00287 (22913) covalent geometry : angle 0.55263 (31506) hydrogen bonds : bond 0.04126 ( 1120) hydrogen bonds : angle 4.23454 ( 3216) Misc. bond : bond 0.03477 ( 29) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.830 Fit side-chains REVERT: D 307 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7504 (mt-10) REVERT: F 39 MET cc_start: 0.8979 (mtt) cc_final: 0.8654 (mtt) REVERT: H 69 ASN cc_start: 0.8959 (t0) cc_final: 0.8588 (t0) REVERT: 3 116 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.5998 (tp40) REVERT: C 189 ASN cc_start: 0.9014 (p0) cc_final: 0.8753 (p0) outliers start: 26 outliers final: 17 residues processed: 178 average time/residue: 0.6595 time to fit residues: 133.9863 Evaluate side-chains 172 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 139 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 185 optimal weight: 0.0570 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN E 61 GLN H 34 ASN G 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.111499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.084812 restraints weight = 33651.108| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.71 r_work: 0.3110 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 22942 Z= 0.198 Angle : 0.594 11.992 31506 Z= 0.276 Chirality : 0.042 0.265 3095 Planarity : 0.005 0.045 3888 Dihedral : 15.076 121.129 4403 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 1.11 % Allowed : 12.63 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.18), residues: 2302 helix: 2.10 (0.14), residues: 1440 sheet: -0.61 (0.85), residues: 37 loop : -0.64 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 23 TYR 0.018 0.001 TYR H 68 PHE 0.016 0.001 PHE B 246 TRP 0.026 0.001 TRP D 14 HIS 0.010 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00471 (22913) covalent geometry : angle 0.59430 (31506) hydrogen bonds : bond 0.04616 ( 1120) hydrogen bonds : angle 4.34188 ( 3216) Misc. bond : bond 0.04219 ( 29) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4604 Ramachandran restraints generated. 2302 Oldfield, 0 Emsley, 2302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.782 Fit side-chains REVERT: D 307 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7512 (mt-10) REVERT: F 39 MET cc_start: 0.8998 (mtt) cc_final: 0.8648 (mtt) REVERT: H 69 ASN cc_start: 0.8965 (t0) cc_final: 0.8584 (t0) REVERT: G 93 LEU cc_start: 0.7556 (tp) cc_final: 0.7260 (mt) REVERT: 3 116 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.5940 (tp40) REVERT: C 189 ASN cc_start: 0.9016 (p0) cc_final: 0.8753 (p0) REVERT: A 293 MET cc_start: 0.8720 (mtm) cc_final: 0.8377 (mtp) outliers start: 21 outliers final: 17 residues processed: 166 average time/residue: 0.6996 time to fit residues: 132.4183 Evaluate side-chains 171 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain T residue 29 MET Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain 3 residue 67 THR Chi-restraints excluded: chain 3 residue 116 GLN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 25 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 203 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 GLN E 61 GLN H 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.113010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086247 restraints weight = 33433.874| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.71 r_work: 0.3138 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.194 22942 Z= 0.128 Angle : 0.557 12.116 31506 Z= 0.260 Chirality : 0.040 0.297 3095 Planarity : 0.004 0.043 3888 Dihedral : 14.884 120.462 4403 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 1.06 % Allowed : 12.79 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.18), residues: 2302 helix: 2.22 (0.14), residues: 1434 sheet: -0.61 (0.84), residues: 37 loop : -0.61 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 23 TYR 0.012 0.001 TYR H 68 PHE 0.014 0.001 PHE I 19 TRP 0.027 0.001 TRP D 14 HIS 0.007 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00287 (22913) covalent geometry : angle 0.55723 (31506) hydrogen bonds : bond 0.04225 ( 1120) hydrogen bonds : angle 4.26417 ( 3216) Misc. bond : bond 0.03625 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8235.67 seconds wall clock time: 140 minutes 52.24 seconds (8452.24 seconds total)