Starting phenix.real_space_refine on Sat Sep 12 05:38:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tfl_25876/09_2026/7tfl_25876.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 209 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 38 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 8526 2.51 5 N 2397 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13690 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2659 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 2 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2581 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2684 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "I" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.15, per 1000 atoms: 0.23 Number of scatterers: 13690 At special positions: 0 Unit cell: (86.94, 119.232, 128.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 38 15.00 Mg 4 11.99 O 2657 8.00 N 2397 7.00 C 8526 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=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 644.0 milliseconds 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 7 sheets defined 64.9% alpha, 5.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.541A pdb=" N SER A 330 " --> pdb=" O TRP A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.617A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.563A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.000A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.891A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 4.331A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.586A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.518A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.554A pdb=" N HIS A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 646 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 removed outlier: 4.056A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.604A pdb=" N SER A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 removed outlier: 3.964A pdb=" N ILE B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.648A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.641A pdb=" N GLN B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.925A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.515A pdb=" N ALA B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.501A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.746A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.519A pdb=" N TYR C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.653A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.513A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.102A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.654A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.689A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.628A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.146A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 removed outlier: 4.327A pdb=" N GLU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.534A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 removed outlier: 3.680A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.789A pdb=" N TYR D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.028A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.015A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 116 " --> pdb=" O ASN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.613A pdb=" N LEU D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.304A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 removed outlier: 3.558A pdb=" N LEU D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.902A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.051A pdb=" N LYS E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 8' Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.035A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.090A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.024A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 removed outlier: 3.583A pdb=" N LYS E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 209 removed outlier: 3.539A pdb=" N ILE E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.858A pdb=" N SER E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.606A pdb=" N LEU E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.842A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.148A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 424 removed outlier: 3.660A pdb=" N ILE A 473 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 352 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.072A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.502A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE C 115 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 82 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.547A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.472A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 61 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 168 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.910A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 139 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4521 1.36 - 1.51: 3565 1.51 - 1.66: 5768 1.66 - 1.80: 61 1.80 - 1.95: 44 Bond restraints: 13959 Sorted by residual: bond pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" C3' DC I 17 " pdb=" C2' DC I 17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.90e+00 bond pdb=" C3' DC I 19 " pdb=" C2' DC I 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C3' DG I 14 " pdb=" C2' DG I 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.16e+00 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.06e+00 ... (remaining 13954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18636 2.09 - 4.18: 307 4.18 - 6.27: 37 6.27 - 8.36: 10 8.36 - 10.46: 4 Bond angle restraints: 18994 Sorted by residual: angle pdb=" CA PRO C 239 " pdb=" N PRO C 239 " pdb=" CD PRO C 239 " ideal model delta sigma weight residual 112.00 105.95 6.05 1.40e+00 5.10e-01 1.87e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.12 116.46 -6.34 1.47e+00 4.63e-01 1.86e+01 angle pdb=" N3 DT I 11 " pdb=" C4 DT I 11 " pdb=" O4 DT I 11 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 18989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 8080 28.10 - 56.19: 391 56.19 - 84.29: 28 84.29 - 112.38: 1 112.38 - 140.48: 2 Dihedral angle restraints: 8502 sinusoidal: 3671 harmonic: 4831 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -172.56 112.56 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" O1A AGS D 500 " pdb=" O3A AGS D 500 " pdb=" PA AGS D 500 " pdb=" PB AGS D 500 " ideal model delta sinusoidal sigma weight residual -67.73 72.75 -140.48 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA PHE A 346 " pdb=" C PHE A 346 " pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1589 0.041 - 0.082: 476 0.082 - 0.123: 127 0.123 - 0.165: 12 0.165 - 0.206: 3 Chirality restraints: 2207 Sorted by residual: chirality pdb=" CG LEU B 313 " pdb=" CB LEU B 313 " pdb=" CD1 LEU B 313 " pdb=" CD2 LEU B 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA LEU A 549 " pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CB LEU A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2204 not shown) Planarity restraints: 2316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 324 " -0.035 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP D 324 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 324 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 324 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 324 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 324 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 324 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 324 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 324 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 324 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 238 " -0.055 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 239 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 449 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 450 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.031 5.00e-02 4.00e+02 ... (remaining 2313 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 237 2.65 - 3.21: 12920 3.21 - 3.78: 22653 3.78 - 4.34: 29629 4.34 - 4.90: 47569 Nonbonded interactions: 113008 Sorted by model distance: nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.089 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.108 2.170 nonbonded pdb=" O3G AGS D 500 " pdb="MG MG E 401 " model vdw 2.111 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.123 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.187 2.170 ... (remaining 113003 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 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 : 0.003 0.110 13959 Z= 0.194 Angle : 0.636 10.456 18994 Z= 0.357 Chirality : 0.042 0.206 2207 Planarity : 0.005 0.080 2316 Dihedral : 14.934 140.476 5360 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1637 helix: 0.92 (0.17), residues: 927 sheet: 0.00 (0.48), residues: 132 loop : -0.22 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 347 TYR 0.014 0.001 TYR E 92 PHE 0.018 0.001 PHE A 346 TRP 0.073 0.002 TRP D 324 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.19 (13959) covalent geometry : angle 0.63552 / 0.36 (18994) hydrogen bonds : bond 0.16972 / 11.14 ( 708) hydrogen bonds : angle 6.00487 / 4.24 ( 2069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LYS cc_start: 0.7309 (pptt) cc_final: 0.6820 (mmtt) REVERT: E 101 MET cc_start: 0.3852 (ppp) cc_final: 0.2887 (ppp) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.0993 time to fit residues: 36.7296 Evaluate side-chains 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS B 26 ASN B 98 GLN B 108 HIS B 155 GLN C 12 ASN C 260 HIS D 209 ASN E 93 HIS E 104 ASN E 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.185572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.164680 restraints weight = 25428.036| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 3.02 r_work: 0.4354 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13959 Z= 0.145 Angle : 0.619 10.308 18994 Z= 0.324 Chirality : 0.042 0.219 2207 Planarity : 0.005 0.042 2316 Dihedral : 12.633 140.046 2092 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 1.10 % Allowed : 8.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1637 helix: 1.00 (0.17), residues: 961 sheet: -0.21 (0.49), residues: 127 loop : -0.15 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 347 TYR 0.019 0.001 TYR D 129 PHE 0.024 0.002 PHE A 419 TRP 0.053 0.002 TRP D 324 HIS 0.007 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (13959) covalent geometry : angle 0.61926 / 0.32 (18994) hydrogen bonds : bond 0.04488 / 2.99 ( 708) hydrogen bonds : angle 4.86964 / 3.44 ( 2069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ASP cc_start: 0.5074 (m-30) cc_final: 0.3517 (p0) REVERT: E 101 MET cc_start: 0.4304 (ppp) cc_final: 0.3015 (ppp) REVERT: E 229 ASN cc_start: 0.7936 (t0) cc_final: 0.7690 (t0) outliers start: 16 outliers final: 7 residues processed: 222 average time/residue: 0.1069 time to fit residues: 36.6234 Evaluate side-chains 192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 141 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 77 optimal weight: 0.3980 chunk 151 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 162 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN C 105 GLN C 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.183963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.162743 restraints weight = 25559.298| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 3.06 r_work: 0.4323 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13959 Z= 0.127 Angle : 0.586 9.337 18994 Z= 0.303 Chirality : 0.041 0.272 2207 Planarity : 0.004 0.040 2316 Dihedral : 12.715 143.834 2092 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 1.58 % Allowed : 11.44 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.21), residues: 1637 helix: 1.17 (0.17), residues: 964 sheet: -0.54 (0.48), residues: 127 loop : -0.14 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 154 TYR 0.019 0.001 TYR D 129 PHE 0.021 0.001 PHE B 196 TRP 0.019 0.001 TRP D 324 HIS 0.005 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (13959) covalent geometry : angle 0.58555 / 0.30 (18994) hydrogen bonds : bond 0.03865 / 2.54 ( 708) hydrogen bonds : angle 4.61905 / 3.25 ( 2069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ASP cc_start: 0.5077 (m-30) cc_final: 0.3562 (p0) REVERT: B 119 MET cc_start: 0.6914 (mtt) cc_final: 0.6635 (mtp) REVERT: C 52 TYR cc_start: 0.6009 (t80) cc_final: 0.5805 (t80) REVERT: E 101 MET cc_start: 0.4353 (ppp) cc_final: 0.3039 (ppp) outliers start: 23 outliers final: 14 residues processed: 218 average time/residue: 0.1055 time to fit residues: 35.0372 Evaluate side-chains 196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 339 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.180999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.159762 restraints weight = 25642.549| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 3.03 r_work: 0.4302 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13959 Z= 0.135 Angle : 0.591 10.271 18994 Z= 0.304 Chirality : 0.041 0.202 2207 Planarity : 0.004 0.040 2316 Dihedral : 12.830 144.860 2092 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 13.01 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1637 helix: 1.16 (0.17), residues: 967 sheet: -0.77 (0.46), residues: 133 loop : -0.13 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 132 TYR 0.018 0.001 TYR D 129 PHE 0.025 0.002 PHE A 419 TRP 0.016 0.001 TRP D 324 HIS 0.004 0.001 HIS C 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13959) covalent geometry : angle 0.59124 / 0.30 (18994) hydrogen bonds : bond 0.03614 / 2.37 ( 708) hydrogen bonds : angle 4.50432 / 3.17 ( 2069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ASP cc_start: 0.5100 (m-30) cc_final: 0.3560 (p0) REVERT: B 119 MET cc_start: 0.6916 (mtt) cc_final: 0.6714 (mtp) REVERT: B 253 ARG cc_start: 0.5220 (mtm110) cc_final: 0.4979 (mtm180) REVERT: C 22 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6636 (mt-10) REVERT: E 101 MET cc_start: 0.4375 (ppp) cc_final: 0.3381 (ppp) outliers start: 22 outliers final: 16 residues processed: 208 average time/residue: 0.1022 time to fit residues: 32.7741 Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.179510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.158178 restraints weight = 25429.703| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.02 r_work: 0.4273 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13959 Z= 0.129 Angle : 0.582 9.566 18994 Z= 0.298 Chirality : 0.041 0.200 2207 Planarity : 0.004 0.043 2316 Dihedral : 12.886 144.062 2092 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 13.22 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1637 helix: 1.24 (0.17), residues: 961 sheet: -1.05 (0.46), residues: 130 loop : -0.03 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.018 0.001 TYR D 129 PHE 0.035 0.002 PHE A 346 TRP 0.010 0.001 TRP D 324 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13959) covalent geometry : angle 0.58156 / 0.30 (18994) hydrogen bonds : bond 0.03467 / 2.28 ( 708) hydrogen bonds : angle 4.41827 / 3.11 ( 2069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.5854 (tmm) cc_final: 0.5651 (tmm) REVERT: A 463 MET cc_start: 0.4190 (mmp) cc_final: 0.2880 (mtt) REVERT: B 83 ASP cc_start: 0.5084 (m-30) cc_final: 0.3594 (p0) REVERT: B 237 LYS cc_start: 0.6226 (mmtp) cc_final: 0.5888 (mmtt) REVERT: B 253 ARG cc_start: 0.5202 (mtm110) cc_final: 0.4982 (mtm180) REVERT: E 101 MET cc_start: 0.4462 (ppp) cc_final: 0.3458 (ppp) outliers start: 30 outliers final: 22 residues processed: 221 average time/residue: 0.0964 time to fit residues: 32.6891 Evaluate side-chains 203 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 20 optimal weight: 0.0010 chunk 160 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.179683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.158198 restraints weight = 25507.330| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.09 r_work: 0.4267 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13959 Z= 0.121 Angle : 0.588 9.858 18994 Z= 0.298 Chirality : 0.041 0.359 2207 Planarity : 0.004 0.047 2316 Dihedral : 12.922 143.148 2092 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1637 helix: 1.29 (0.17), residues: 960 sheet: -0.94 (0.47), residues: 128 loop : -0.00 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 331 TYR 0.019 0.001 TYR D 129 PHE 0.027 0.002 PHE D 203 TRP 0.009 0.001 TRP D 324 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13959) covalent geometry : angle 0.58831 / 0.30 (18994) hydrogen bonds : bond 0.03350 / 2.21 ( 708) hydrogen bonds : angle 4.39689 / 3.10 ( 2069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4255 (mmp) cc_final: 0.2991 (mtt) REVERT: B 83 ASP cc_start: 0.5113 (m-30) cc_final: 0.3609 (p0) REVERT: B 114 ASP cc_start: 0.4170 (OUTLIER) cc_final: 0.3316 (t0) REVERT: B 253 ARG cc_start: 0.5244 (mtm110) cc_final: 0.5037 (mtm180) REVERT: C 22 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6738 (mt-10) REVERT: D 228 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6192 (tt) REVERT: E 101 MET cc_start: 0.4646 (ppp) cc_final: 0.3620 (ppp) outliers start: 29 outliers final: 21 residues processed: 214 average time/residue: 0.0985 time to fit residues: 33.2606 Evaluate side-chains 205 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 75 optimal weight: 0.1980 chunk 43 optimal weight: 0.0000 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.179556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.158259 restraints weight = 25501.897| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 3.03 r_work: 0.4269 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13959 Z= 0.120 Angle : 0.589 9.683 18994 Z= 0.298 Chirality : 0.040 0.166 2207 Planarity : 0.004 0.044 2316 Dihedral : 12.956 141.873 2092 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.33 % Allowed : 14.59 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1637 helix: 1.34 (0.17), residues: 960 sheet: -0.96 (0.47), residues: 128 loop : 0.05 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.019 0.001 TYR D 129 PHE 0.025 0.001 PHE A 346 TRP 0.010 0.001 TRP D 324 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13959) covalent geometry : angle 0.58929 / 0.30 (18994) hydrogen bonds : bond 0.03302 / 2.17 ( 708) hydrogen bonds : angle 4.34494 / 3.05 ( 2069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4129 (mmp) cc_final: 0.3007 (mtt) REVERT: B 83 ASP cc_start: 0.5084 (m-30) cc_final: 0.3623 (p0) REVERT: B 114 ASP cc_start: 0.4091 (OUTLIER) cc_final: 0.3322 (t0) REVERT: B 119 MET cc_start: 0.6424 (mtt) cc_final: 0.6204 (mtp) REVERT: C 22 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6770 (mt-10) REVERT: D 228 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6232 (tt) REVERT: E 101 MET cc_start: 0.4606 (ppp) cc_final: 0.3628 (ppp) REVERT: E 229 ASN cc_start: 0.8199 (t0) cc_final: 0.7906 (t0) REVERT: E 299 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7384 (mp) outliers start: 34 outliers final: 25 residues processed: 214 average time/residue: 0.1020 time to fit residues: 34.1241 Evaluate side-chains 215 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 HIS ** C 12 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 = 0.4657 r_free = 0.4657 target = 0.177215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.155592 restraints weight = 25432.194| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.06 r_work: 0.4244 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13959 Z= 0.136 Angle : 0.604 10.122 18994 Z= 0.307 Chirality : 0.042 0.212 2207 Planarity : 0.004 0.043 2316 Dihedral : 13.042 144.823 2092 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.53 % Allowed : 14.38 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1637 helix: 1.21 (0.17), residues: 977 sheet: -1.08 (0.46), residues: 128 loop : 0.01 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.018 0.001 TYR D 129 PHE 0.029 0.002 PHE D 203 TRP 0.006 0.001 TRP D 324 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (13959) covalent geometry : angle 0.60443 / 0.31 (18994) hydrogen bonds : bond 0.03443 / 2.26 ( 708) hydrogen bonds : angle 4.36690 / 3.08 ( 2069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4193 (mmp) cc_final: 0.3173 (mtt) REVERT: B 83 ASP cc_start: 0.5110 (m-30) cc_final: 0.3655 (p0) REVERT: B 114 ASP cc_start: 0.4380 (OUTLIER) cc_final: 0.3278 (t0) REVERT: C 22 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6868 (mt-10) REVERT: D 228 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6267 (tt) REVERT: E 101 MET cc_start: 0.4683 (ppp) cc_final: 0.3633 (ppp) REVERT: E 299 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7421 (mp) outliers start: 37 outliers final: 26 residues processed: 218 average time/residue: 0.1053 time to fit residues: 35.6738 Evaluate side-chains 215 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 46 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.177596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.156030 restraints weight = 25479.747| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.06 r_work: 0.4242 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13959 Z= 0.123 Angle : 0.604 9.806 18994 Z= 0.302 Chirality : 0.041 0.286 2207 Planarity : 0.004 0.045 2316 Dihedral : 13.046 142.202 2092 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1637 helix: 1.29 (0.17), residues: 971 sheet: -1.06 (0.46), residues: 128 loop : 0.04 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 156 TYR 0.019 0.001 TYR D 129 PHE 0.023 0.001 PHE A 346 TRP 0.009 0.001 TRP E 4 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13959) covalent geometry : angle 0.60372 / 0.30 (18994) hydrogen bonds : bond 0.03303 / 2.17 ( 708) hydrogen bonds : angle 4.32357 / 3.04 ( 2069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ASP cc_start: 0.5123 (m-30) cc_final: 0.3660 (p0) REVERT: B 119 MET cc_start: 0.6676 (mtt) cc_final: 0.6211 (mtm) REVERT: C 22 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6842 (mt-10) REVERT: D 228 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6183 (tt) REVERT: E 101 MET cc_start: 0.4699 (ppp) cc_final: 0.3673 (ppp) REVERT: E 246 LEU cc_start: 0.8183 (pp) cc_final: 0.7856 (tt) REVERT: E 299 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7333 (mp) outliers start: 29 outliers final: 25 residues processed: 205 average time/residue: 0.1041 time to fit residues: 33.3183 Evaluate side-chains 206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 58 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 43 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.177882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156560 restraints weight = 25389.501| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.99 r_work: 0.4259 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13959 Z= 0.124 Angle : 0.620 13.629 18994 Z= 0.309 Chirality : 0.041 0.261 2207 Planarity : 0.004 0.045 2316 Dihedral : 13.062 141.727 2092 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.12 % Allowed : 15.07 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1637 helix: 1.34 (0.17), residues: 964 sheet: -1.09 (0.46), residues: 128 loop : 0.03 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 183 TYR 0.020 0.001 TYR D 129 PHE 0.031 0.002 PHE D 203 TRP 0.016 0.001 TRP D 324 HIS 0.004 0.001 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13959) covalent geometry : angle 0.61984 / 0.31 (18994) hydrogen bonds : bond 0.03287 / 2.16 ( 708) hydrogen bonds : angle 4.28884 / 3.02 ( 2069) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.3899 (mmp) cc_final: 0.2755 (mtt) REVERT: B 83 ASP cc_start: 0.5137 (m-30) cc_final: 0.3683 (p0) REVERT: B 119 MET cc_start: 0.6670 (mtt) cc_final: 0.6228 (mtm) REVERT: C 22 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6850 (mt-10) REVERT: E 101 MET cc_start: 0.4618 (ppp) cc_final: 0.3624 (ppp) REVERT: E 246 LEU cc_start: 0.8178 (pp) cc_final: 0.7862 (tt) REVERT: E 299 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7284 (mp) outliers start: 31 outliers final: 26 residues processed: 204 average time/residue: 0.1033 time to fit residues: 32.7309 Evaluate side-chains 206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.176215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.154901 restraints weight = 25534.132| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.98 r_work: 0.4242 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13959 Z= 0.139 Angle : 0.634 11.852 18994 Z= 0.318 Chirality : 0.042 0.272 2207 Planarity : 0.004 0.044 2316 Dihedral : 13.121 144.127 2092 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.05 % Allowed : 15.41 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1637 helix: 1.21 (0.17), residues: 971 sheet: -1.16 (0.46), residues: 128 loop : -0.06 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 296 TYR 0.019 0.001 TYR D 129 PHE 0.029 0.002 PHE D 203 TRP 0.019 0.001 TRP D 324 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13959) covalent geometry : angle 0.63399 / 0.32 (18994) hydrogen bonds : bond 0.03392 / 2.23 ( 708) hydrogen bonds : angle 4.35487 / 3.07 ( 2069) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3107.65 seconds wall clock time: 54 minutes 21.30 seconds (3261.30 seconds total)