Starting phenix.real_space_refine on Wed May 21 20:28:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kde_37133/05_2025/8kde_37133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kde_37133/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kde_37133/05_2025/8kde_37133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kde_37133/05_2025/8kde_37133.map" model { file = "/net/cci-nas-00/data/ceres_data/8kde_37133/05_2025/8kde_37133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kde_37133/05_2025/8kde_37133_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.16, per 1000 atoms: 0.60 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: 7.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.01 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: 6.15 Time building geometry restraints manager: 8.22 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: 3.080 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: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 48.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- 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 : 4.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (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 TRP 0.011 0.001 TRP B 247 HIS 0.008 0.001 HIS 1 60 PHE 0.032 0.001 PHE B 250 TYR 0.011 0.001 TYR A 126 ARG 0.005 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.12723 ( 1120) hydrogen bonds : angle 5.95484 ( 3216) covalent geometry : bond 0.00736 (22913) covalent geometry : angle 1.17739 (31506) 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 : 2.099 Fit side-chains revert: symmetry clash 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: 0.6571 (ttmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 1.4147 time to fit residues: 292.1227 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 : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** C 62 HIS A 187 GLN A 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.113771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087549 restraints weight = 33097.791| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.69 r_work: 0.3153 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 22942 Z= 0.145 Angle : 0.633 15.393 31506 Z= 0.287 Chirality : 0.042 0.358 3095 Planarity : 0.005 0.043 3888 Dihedral : 16.800 121.691 4403 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 1.06 % Allowed : 6.05 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2302 helix: 2.06 (0.14), residues: 1440 sheet: -0.72 (0.84), residues: 37 loop : -0.66 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 167 HIS 0.006 0.001 HIS C 418 PHE 0.013 0.001 PHE A 295 TYR 0.021 0.001 TYR H 68 ARG 0.008 0.000 ARG B 472 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 1120) hydrogen bonds : angle 4.70773 ( 3216) covalent geometry : bond 0.00318 (22913) covalent geometry : angle 0.63280 (31506) Misc. bond : bond 0.04535 ( 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 173 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 2.073 Fit side-chains REVERT: B 256 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8604 (tpp) REVERT: D 265 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7636 (ttp80) REVERT: D 301 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8264 (tp40) REVERT: F 39 MET cc_start: 0.8983 (mtt) cc_final: 0.8644 (mtt) REVERT: G 93 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7086 (mt) REVERT: C 444 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: A 199 MET cc_start: 0.8956 (mtt) cc_final: 0.8719 (mtm) outliers start: 20 outliers final: 3 residues processed: 163 average time/residue: 1.4029 time to fit residues: 260.4661 Evaluate side-chains 147 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 444 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 118 optimal weight: 0.8980 chunk 133 optimal weight: 0.0670 chunk 125 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 188 optimal weight: 0.7980 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** B 394 GLN D 164 GLN A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087591 restraints weight = 32899.532| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.70 r_work: 0.3156 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.195 22942 Z= 0.134 Angle : 0.570 12.360 31506 Z= 0.261 Chirality : 0.040 0.329 3095 Planarity : 0.004 0.041 3888 Dihedral : 15.431 120.425 4403 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.44 % Rotamer: Outliers : 1.43 % Allowed : 7.91 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2302 helix: 2.16 (0.14), residues: 1429 sheet: -0.53 (0.87), residues: 37 loop : -0.64 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 247 HIS 0.005 0.001 HIS C 418 PHE 0.013 0.001 PHE D 113 TYR 0.015 0.001 TYR H 68 ARG 0.006 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1120) hydrogen bonds : angle 4.47758 ( 3216) covalent geometry : bond 0.00298 (22913) covalent geometry : angle 0.57039 (31506) Misc. bond : bond 0.03681 ( 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 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 2.073 Fit side-chains REVERT: B 256 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8576 (tpp) REVERT: D 265 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7649 (ttp80) REVERT: D 301 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8242 (tp40) REVERT: D 307 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7445 (mt-10) REVERT: F 39 MET cc_start: 0.8988 (mtt) cc_final: 0.8677 (mtt) REVERT: H 69 ASN cc_start: 0.9006 (t0) cc_final: 0.8575 (t0) REVERT: G 93 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7191 (mt) REVERT: C 189 ASN cc_start: 0.9023 (p0) cc_final: 0.8675 (p0) outliers start: 27 outliers final: 7 residues processed: 169 average time/residue: 1.3643 time to fit residues: 264.0912 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 : 2.029 ------------------------------------------------------------------------------- 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 158 LEU 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 10 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 80 GLN A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.085560 restraints weight = 33532.745| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.70 r_work: 0.3119 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 22942 Z= 0.188 Angle : 0.594 11.726 31506 Z= 0.274 Chirality : 0.042 0.312 3095 Planarity : 0.005 0.043 3888 Dihedral : 15.449 121.499 4403 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 1.43 % Allowed : 8.86 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2302 helix: 2.04 (0.14), residues: 1438 sheet: -0.47 (0.89), residues: 37 loop : -0.71 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 247 HIS 0.006 0.001 HIS C 418 PHE 0.014 0.001 PHE B 246 TYR 0.023 0.001 TYR H 68 ARG 0.005 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 1120) hydrogen bonds : angle 4.48388 ( 3216) covalent geometry : bond 0.00444 (22913) covalent geometry : angle 0.59405 (31506) Misc. bond : bond 0.04302 ( 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 187 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 2.064 Fit side-chains REVERT: B 256 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8651 (tpp) REVERT: D 265 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7741 (ttp80) REVERT: D 301 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8247 (tp40) REVERT: D 307 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7466 (mt-10) REVERT: F 39 MET cc_start: 0.9029 (mtt) cc_final: 0.8690 (mtt) REVERT: H 69 ASN cc_start: 0.9007 (t0) cc_final: 0.8563 (t0) REVERT: C 187 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8616 (mm) REVERT: C 189 ASN cc_start: 0.9052 (p0) cc_final: 0.8710 (p0) REVERT: C 408 VAL cc_start: 0.8384 (t) cc_final: 0.8099 (m) outliers start: 27 outliers final: 13 residues processed: 172 average time/residue: 1.3053 time to fit residues: 258.0251 Evaluate side-chains 172 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 217 LEU 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 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 G residue 60 LEU Chi-restraints excluded: chain G residue 107 LEU 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 6 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 F 23 HIS H 34 ASN ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085699 restraints weight = 33610.692| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.70 r_work: 0.3120 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1505 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 : 0.563 11.125 31506 Z= 0.261 Chirality : 0.041 0.266 3095 Planarity : 0.004 0.044 3888 Dihedral : 15.288 120.893 4403 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 9.93 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2302 helix: 2.10 (0.14), residues: 1432 sheet: -0.53 (0.86), residues: 37 loop : -0.66 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 247 HIS 0.005 0.001 HIS C 418 PHE 0.014 0.001 PHE B 246 TYR 0.018 0.001 TYR H 68 ARG 0.004 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 1120) hydrogen bonds : angle 4.38410 ( 3216) covalent geometry : bond 0.00370 (22913) covalent geometry : angle 0.56326 (31506) Misc. bond : bond 0.03808 ( 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 194 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 2.069 Fit side-chains REVERT: B 256 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8657 (tpp) REVERT: D 301 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8227 (tp40) REVERT: D 307 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7515 (mt-10) REVERT: F 39 MET cc_start: 0.8981 (mtt) cc_final: 0.8640 (mtt) REVERT: H 69 ASN cc_start: 0.8998 (t0) cc_final: 0.8642 (t0) REVERT: C 408 VAL cc_start: 0.8366 (t) cc_final: 0.8073 (m) outliers start: 34 outliers final: 16 residues processed: 181 average time/residue: 1.2608 time to fit residues: 263.3648 Evaluate side-chains 166 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 256 MET 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 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 190 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 130 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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** H 34 ASN ** H 69 ASN ** 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 = 0.3673 r_free = 0.3673 target = 0.111798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.085224 restraints weight = 33405.291| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.70 r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 22942 Z= 0.173 Angle : 0.579 11.078 31506 Z= 0.268 Chirality : 0.041 0.262 3095 Planarity : 0.005 0.044 3888 Dihedral : 15.256 121.156 4403 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 1.70 % Allowed : 10.40 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2302 helix: 2.09 (0.14), residues: 1432 sheet: -0.53 (0.86), residues: 37 loop : -0.67 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 14 HIS 0.006 0.001 HIS C 418 PHE 0.015 0.001 PHE B 246 TYR 0.017 0.001 TYR H 68 ARG 0.008 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1120) hydrogen bonds : angle 4.38045 ( 3216) covalent geometry : bond 0.00405 (22913) covalent geometry : angle 0.57874 (31506) Misc. bond : bond 0.03951 ( 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 201 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 2.017 Fit side-chains REVERT: B 256 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: B 429 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8811 (mm) REVERT: D 301 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8237 (tp40) REVERT: D 307 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7538 (mt-10) REVERT: F 39 MET cc_start: 0.8999 (mtt) cc_final: 0.8654 (mtt) REVERT: H 69 ASN cc_start: 0.8993 (t0) cc_final: 0.8650 (t0) REVERT: C 187 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8654 (mm) REVERT: C 189 ASN cc_start: 0.9030 (p0) cc_final: 0.8715 (p0) outliers start: 32 outliers final: 17 residues processed: 189 average time/residue: 1.2084 time to fit residues: 264.5610 Evaluate side-chains 187 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 256 MET 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 B residue 429 ILE 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 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 Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 130 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 127 optimal weight: 0.0020 chunk 63 optimal weight: 1.9990 chunk 180 optimal weight: 0.0010 chunk 209 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 226 optimal weight: 8.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 301 GLN H 34 ASN A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087421 restraints weight = 33371.385| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.72 r_work: 0.3157 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 22942 Z= 0.113 Angle : 0.537 10.972 31506 Z= 0.249 Chirality : 0.039 0.239 3095 Planarity : 0.004 0.044 3888 Dihedral : 14.933 119.675 4403 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 1.49 % Allowed : 11.31 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 2302 helix: 2.24 (0.14), residues: 1438 sheet: -0.55 (0.84), residues: 37 loop : -0.61 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 14 HIS 0.004 0.001 HIS D 268 PHE 0.012 0.001 PHE B 139 TYR 0.010 0.001 TYR H 68 ARG 0.008 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1120) hydrogen bonds : angle 4.22501 ( 3216) covalent geometry : bond 0.00243 (22913) covalent geometry : angle 0.53714 (31506) Misc. bond : bond 0.03259 ( 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 199 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.174 Fit side-chains REVERT: B 256 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8526 (tpp) REVERT: D 307 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7506 (mt-10) REVERT: F 39 MET cc_start: 0.8950 (mtt) cc_final: 0.8610 (mtp) REVERT: H 69 ASN cc_start: 0.8925 (t0) cc_final: 0.8706 (t0) REVERT: C 189 ASN cc_start: 0.9014 (p0) cc_final: 0.8718 (p0) outliers start: 28 outliers final: 15 residues processed: 186 average time/residue: 1.2412 time to fit residues: 266.8173 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 : 2.063 ------------------------------------------------------------------------------- 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 256 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 88 optimal weight: 0.0070 chunk 185 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- 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 A 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.112898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086122 restraints weight = 33571.887| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.72 r_work: 0.3134 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 22942 Z= 0.144 Angle : 0.555 10.996 31506 Z= 0.260 Chirality : 0.040 0.253 3095 Planarity : 0.004 0.044 3888 Dihedral : 14.928 120.412 4403 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 11.84 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2302 helix: 2.19 (0.14), residues: 1433 sheet: -0.63 (0.84), residues: 37 loop : -0.61 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 14 HIS 0.005 0.001 HIS C 418 PHE 0.020 0.001 PHE B 246 TYR 0.014 0.001 TYR H 68 ARG 0.008 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 1120) hydrogen bonds : angle 4.25220 ( 3216) covalent geometry : bond 0.00330 (22913) covalent geometry : angle 0.55469 (31506) Misc. bond : bond 0.03678 ( 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 188 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.864 Fit side-chains REVERT: B 256 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8599 (tpp) REVERT: D 307 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7505 (mt-10) REVERT: F 39 MET cc_start: 0.8992 (mtt) cc_final: 0.8662 (mtt) REVERT: H 69 ASN cc_start: 0.8953 (t0) cc_final: 0.8721 (t0) REVERT: C 189 ASN cc_start: 0.9014 (p0) cc_final: 0.8734 (p0) REVERT: C 408 VAL cc_start: 0.8380 (t) cc_final: 0.8073 (m) outliers start: 27 outliers final: 16 residues processed: 175 average time/residue: 1.2436 time to fit residues: 251.7916 Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 2.087 ------------------------------------------------------------------------------- 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 256 MET 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 107 LEU Chi-restraints excluded: chain 3 residue 67 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 161 optimal weight: 3.9990 chunk 82 optimal weight: 0.0470 chunk 140 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084486 restraints weight = 33551.976| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.71 r_work: 0.3108 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 22942 Z= 0.197 Angle : 0.592 11.163 31506 Z= 0.276 Chirality : 0.042 0.265 3095 Planarity : 0.005 0.045 3888 Dihedral : 15.150 121.335 4403 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 1.38 % Allowed : 12.05 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2302 helix: 2.09 (0.14), residues: 1436 sheet: -0.58 (0.85), residues: 37 loop : -0.67 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 14 HIS 0.006 0.001 HIS A 195 PHE 0.019 0.001 PHE B 246 TYR 0.018 0.001 TYR H 68 ARG 0.008 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1120) hydrogen bonds : angle 4.35737 ( 3216) covalent geometry : bond 0.00468 (22913) covalent geometry : angle 0.59181 (31506) Misc. bond : bond 0.04297 ( 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 183 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.081 Fit side-chains REVERT: B 256 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8680 (tpp) REVERT: D 307 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7504 (mt-10) REVERT: F 39 MET cc_start: 0.9008 (mtt) cc_final: 0.8664 (mtt) REVERT: H 69 ASN cc_start: 0.8959 (t0) cc_final: 0.8657 (t0) REVERT: C 189 ASN cc_start: 0.9011 (p0) cc_final: 0.8744 (p0) outliers start: 26 outliers final: 17 residues processed: 173 average time/residue: 1.2728 time to fit residues: 254.5537 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 : 2.114 ------------------------------------------------------------------------------- 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 256 MET 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 72 ASN 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 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 40 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 G 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085700 restraints weight = 33626.187| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.73 r_work: 0.3128 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.195 22942 Z= 0.146 Angle : 0.563 11.036 31506 Z= 0.263 Chirality : 0.041 0.247 3095 Planarity : 0.004 0.044 3888 Dihedral : 14.980 120.536 4403 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 1.17 % Allowed : 12.37 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2302 helix: 2.12 (0.14), residues: 1446 sheet: -0.61 (0.84), residues: 37 loop : -0.66 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 14 HIS 0.006 0.001 HIS A 195 PHE 0.014 0.001 PHE I 19 TYR 0.012 0.001 TYR H 68 ARG 0.009 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 1120) hydrogen bonds : angle 4.28199 ( 3216) covalent geometry : bond 0.00337 (22913) covalent geometry : angle 0.56268 (31506) Misc. bond : bond 0.03653 ( 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 181 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.963 Fit side-chains REVERT: B 256 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8625 (tpp) REVERT: D 307 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7520 (mt-10) REVERT: F 39 MET cc_start: 0.9000 (mtt) cc_final: 0.8680 (mtt) REVERT: H 69 ASN cc_start: 0.8935 (t0) cc_final: 0.8625 (t0) REVERT: C 189 ASN cc_start: 0.9017 (p0) cc_final: 0.8758 (p0) outliers start: 22 outliers final: 17 residues processed: 170 average time/residue: 1.3020 time to fit residues: 254.1652 Evaluate side-chains 177 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 256 MET 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 72 ASN 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 G residue 107 LEU 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 76 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.085744 restraints weight = 33502.244| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.72 r_work: 0.3129 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.004 0.194 22942 Z= 0.147 Angle : 0.565 13.626 31506 Z= 0.264 Chirality : 0.041 0.250 3095 Planarity : 0.004 0.044 3888 Dihedral : 14.928 120.596 4403 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 12.42 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2302 helix: 2.13 (0.14), residues: 1446 sheet: -0.60 (0.85), residues: 37 loop : -0.67 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 14 HIS 0.007 0.001 HIS A 195 PHE 0.014 0.001 PHE I 19 TYR 0.014 0.001 TYR H 68 ARG 0.009 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 1120) hydrogen bonds : angle 4.27402 ( 3216) covalent geometry : bond 0.00340 (22913) covalent geometry : angle 0.56549 (31506) Misc. bond : bond 0.03646 ( 29) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14988.87 seconds wall clock time: 258 minutes 42.43 seconds (15522.43 seconds total)