Starting phenix.real_space_refine on Thu Jun 12 14:59:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfl_25876/06_2025/7tfl_25876.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfl_25876/06_2025/7tfl_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_25876/06_2025/7tfl_25876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfl_25876/06_2025/7tfl_25876.map" model { file = "/net/cci-nas-00/data/ceres_data/7tfl_25876/06_2025/7tfl_25876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfl_25876/06_2025/7tfl_25876.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.35, per 1000 atoms: 0.68 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: 4.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.03 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: 4.51 Time building geometry restraints manager: 4.45 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=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N LEU A 549 " pdb=" CA LEU A 549 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N ALA A 548 " pdb=" CA ALA A 548 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.70e+00 bond pdb=" N LYS A 550 " pdb=" CA LYS A 550 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.22e+00 ... (remaining 13954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18668 2.09 - 4.18: 275 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=" C ILE B 151 " pdb=" N GLU B 152 " pdb=" CA GLU B 152 " ideal model delta sigma weight residual 120.09 125.11 -5.02 1.25e+00 6.40e-01 1.62e+01 angle pdb=" CA ILE A 547 " pdb=" C ILE A 547 " pdb=" O ILE A 547 " ideal model delta sigma weight residual 121.63 118.04 3.59 9.90e-01 1.02e+00 1.31e+01 angle pdb=" CB LYS D 111 " pdb=" CG LYS D 111 " pdb=" CD LYS D 111 " ideal model delta sigma weight residual 111.30 119.46 -8.16 2.30e+00 1.89e-01 1.26e+01 ... (remaining 18989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 8109 28.10 - 56.19: 403 56.19 - 84.29: 31 84.29 - 112.38: 1 112.38 - 140.48: 2 Dihedral angle restraints: 8546 sinusoidal: 3715 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 8543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1616 0.041 - 0.082: 464 0.082 - 0.123: 112 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 39.200 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 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= 0.135 Angle : 0.621 10.456 18994 Z= 0.316 Chirality : 0.041 0.206 2207 Planarity : 0.005 0.080 2316 Dihedral : 15.097 140.476 5404 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 TRP 0.073 0.002 TRP D 324 HIS 0.005 0.001 HIS D 340 PHE 0.018 0.001 PHE A 346 TYR 0.014 0.001 TYR E 92 ARG 0.007 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.16972 ( 708) hydrogen bonds : angle 6.00487 ( 2069) covalent geometry : bond 0.00270 (13959) covalent geometry : angle 0.62123 (18994) *********************** 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 : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LYS cc_start: 0.7309 (pptt) cc_final: 0.6821 (mmtt) REVERT: E 101 MET cc_start: 0.3852 (ppp) cc_final: 0.2888 (ppp) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.2242 time to fit residues: 81.1044 Evaluate side-chains 178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 26 ASN B 98 GLN B 108 HIS C 12 ASN C 105 GLN C 260 HIS E 93 HIS E 104 ASN E 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.183712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.162583 restraints weight = 25215.054| |-----------------------------------------------------------------------------| r_work (start): 0.4454 rms_B_bonded: 3.01 r_work: 0.4328 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13959 Z= 0.144 Angle : 0.603 9.561 18994 Z= 0.311 Chirality : 0.041 0.142 2207 Planarity : 0.005 0.046 2316 Dihedral : 12.878 143.690 2136 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.51 % Allowed : 8.42 % Favored : 90.07 % 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: 0.71 (0.21), residues: 1637 helix: 1.01 (0.17), residues: 962 sheet: -0.25 (0.49), residues: 127 loop : -0.14 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 324 HIS 0.008 0.001 HIS B 108 PHE 0.022 0.002 PHE A 443 TYR 0.017 0.001 TYR D 129 ARG 0.004 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 708) hydrogen bonds : angle 4.75246 ( 2069) covalent geometry : bond 0.00317 (13959) covalent geometry : angle 0.60279 (18994) *********************** 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 233 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 101 MET cc_start: 0.4306 (ppp) cc_final: 0.3262 (ppp) REVERT: E 229 ASN cc_start: 0.7954 (t0) cc_final: 0.7748 (t0) outliers start: 22 outliers final: 13 residues processed: 224 average time/residue: 0.2521 time to fit residues: 83.8266 Evaluate side-chains 196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.0010 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 155 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 = 0.4702 r_free = 0.4702 target = 0.181698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.160468 restraints weight = 25543.731| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 3.05 r_work: 0.4293 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.1877 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= 0.130 Angle : 0.576 7.950 18994 Z= 0.295 Chirality : 0.040 0.168 2207 Planarity : 0.004 0.038 2316 Dihedral : 12.907 144.582 2136 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.64 % Allowed : 11.58 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1637 helix: 1.16 (0.17), residues: 965 sheet: -0.67 (0.47), residues: 134 loop : -0.10 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 327 HIS 0.008 0.001 HIS C 298 PHE 0.024 0.002 PHE D 290 TYR 0.016 0.001 TYR D 129 ARG 0.004 0.000 ARG E 331 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 708) hydrogen bonds : angle 4.52582 ( 2069) covalent geometry : bond 0.00284 (13959) covalent geometry : angle 0.57615 (18994) *********************** 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 230 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4133 (mmp) cc_final: 0.2862 (mmm) REVERT: B 83 ASP cc_start: 0.5127 (m-30) cc_final: 0.3545 (p0) REVERT: B 119 MET cc_start: 0.6966 (mtt) cc_final: 0.6730 (mtp) REVERT: B 180 LYS cc_start: 0.7338 (pptt) cc_final: 0.7093 (pptt) REVERT: E 101 MET cc_start: 0.4374 (ppp) cc_final: 0.3338 (ppp) outliers start: 24 outliers final: 15 residues processed: 222 average time/residue: 0.2313 time to fit residues: 77.7552 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR 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 D residue 53 LEU 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 254 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 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.179670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.157999 restraints weight = 25246.851| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.13 r_work: 0.4273 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13959 Z= 0.128 Angle : 0.576 9.984 18994 Z= 0.293 Chirality : 0.040 0.237 2207 Planarity : 0.004 0.040 2316 Dihedral : 12.934 143.564 2136 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 1.64 % Allowed : 13.49 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1637 helix: 1.26 (0.17), residues: 961 sheet: -0.90 (0.46), residues: 140 loop : -0.07 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.007 0.001 HIS C 298 PHE 0.025 0.002 PHE D 203 TYR 0.016 0.001 TYR D 129 ARG 0.004 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 708) hydrogen bonds : angle 4.43688 ( 2069) covalent geometry : bond 0.00283 (13959) covalent geometry : angle 0.57648 (18994) *********************** 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 217 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ASP cc_start: 0.5119 (m-30) cc_final: 0.3561 (p0) REVERT: B 180 LYS cc_start: 0.7382 (pptt) cc_final: 0.7167 (pptt) REVERT: C 22 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6750 (mt-10) REVERT: E 101 MET cc_start: 0.4413 (ppp) cc_final: 0.3418 (ppp) outliers start: 24 outliers final: 17 residues processed: 210 average time/residue: 0.4030 time to fit residues: 133.1153 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 252 LEU Chi-restraints excluded: chain B residue 305 THR 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 53 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 52 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 151 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 144 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN B 98 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.178958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.157500 restraints weight = 25345.794| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.08 r_work: 0.4267 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13959 Z= 0.118 Angle : 0.569 8.922 18994 Z= 0.289 Chirality : 0.040 0.218 2207 Planarity : 0.004 0.042 2316 Dihedral : 12.911 140.762 2136 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.99 % Allowed : 13.70 % Favored : 84.32 % 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: 1.00 (0.22), residues: 1637 helix: 1.37 (0.17), residues: 960 sheet: -0.98 (0.45), residues: 140 loop : -0.01 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.006 0.001 HIS C 298 PHE 0.030 0.002 PHE A 346 TYR 0.017 0.001 TYR D 129 ARG 0.005 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 708) hydrogen bonds : angle 4.35323 ( 2069) covalent geometry : bond 0.00262 (13959) covalent geometry : angle 0.56924 (18994) *********************** 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 221 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4054 (mmp) cc_final: 0.2894 (mtt) REVERT: A 596 TYR cc_start: 0.6583 (p90) cc_final: 0.6140 (p90) REVERT: B 83 ASP cc_start: 0.5113 (m-30) cc_final: 0.3527 (p0) REVERT: E 101 MET cc_start: 0.4638 (ppp) cc_final: 0.3638 (ppp) REVERT: E 287 TYR cc_start: 0.7292 (m-80) cc_final: 0.6834 (m-80) outliers start: 29 outliers final: 18 residues processed: 215 average time/residue: 0.2266 time to fit residues: 73.6371 Evaluate side-chains 197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR 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 123 THR 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 53 LEU Chi-restraints excluded: chain D residue 79 THR 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 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.176588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.154873 restraints weight = 25897.106| |-----------------------------------------------------------------------------| r_work (start): 0.4354 rms_B_bonded: 3.11 r_work: 0.4221 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13959 Z= 0.142 Angle : 0.601 9.078 18994 Z= 0.304 Chirality : 0.041 0.185 2207 Planarity : 0.004 0.042 2316 Dihedral : 13.052 144.063 2136 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.33 % Allowed : 14.18 % Favored : 83.49 % 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: 0.85 (0.22), residues: 1637 helix: 1.21 (0.17), residues: 978 sheet: -1.20 (0.46), residues: 130 loop : -0.02 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 324 HIS 0.006 0.001 HIS C 298 PHE 0.026 0.002 PHE D 203 TYR 0.017 0.001 TYR D 129 ARG 0.004 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 708) hydrogen bonds : angle 4.37074 ( 2069) covalent geometry : bond 0.00323 (13959) covalent geometry : angle 0.60076 (18994) *********************** 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 227 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4271 (mmp) cc_final: 0.3189 (mtt) REVERT: A 596 TYR cc_start: 0.6651 (p90) cc_final: 0.6317 (p90) REVERT: B 83 ASP cc_start: 0.5232 (m-30) cc_final: 0.3711 (p0) REVERT: C 22 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6791 (mt-10) REVERT: D 228 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.6202 (tt) REVERT: E 101 MET cc_start: 0.4747 (ppp) cc_final: 0.3706 (ppp) REVERT: E 229 ASN cc_start: 0.8240 (t0) cc_final: 0.8011 (t0) REVERT: E 331 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6797 (mtt-85) outliers start: 34 outliers final: 21 residues processed: 217 average time/residue: 0.2640 time to fit residues: 87.4114 Evaluate side-chains 202 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR 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 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 7 optimal weight: 0.0870 chunk 99 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.0050 chunk 90 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.178438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.157016 restraints weight = 25335.790| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.05 r_work: 0.4256 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.2738 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= 0.117 Angle : 0.601 10.378 18994 Z= 0.300 Chirality : 0.040 0.280 2207 Planarity : 0.004 0.044 2316 Dihedral : 12.972 137.751 2136 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.78 % Allowed : 15.82 % Favored : 82.40 % 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: 1.03 (0.22), residues: 1637 helix: 1.35 (0.17), residues: 970 sheet: -1.11 (0.46), residues: 130 loop : 0.11 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 324 HIS 0.004 0.001 HIS A 610 PHE 0.029 0.002 PHE D 203 TYR 0.016 0.001 TYR D 129 ARG 0.004 0.000 ARG D 183 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 708) hydrogen bonds : angle 4.31309 ( 2069) covalent geometry : bond 0.00258 (13959) covalent geometry : angle 0.60134 (18994) *********************** 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 212 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4197 (mmp) cc_final: 0.3224 (mtt) REVERT: A 655 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7249 (mmmm) REVERT: B 83 ASP cc_start: 0.5196 (m-30) cc_final: 0.3687 (p0) REVERT: B 119 MET cc_start: 0.6815 (mtt) cc_final: 0.6239 (mtm) REVERT: C 22 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6842 (mt-10) REVERT: D 350 ILE cc_start: 0.7826 (pt) cc_final: 0.7587 (mt) REVERT: E 101 MET cc_start: 0.4634 (ppp) cc_final: 0.3624 (ppp) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.2887 time to fit residues: 86.7076 Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 217 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 246 LEU 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 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4655 r_free = 0.4655 target = 0.177287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.155793 restraints weight = 25459.962| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 3.05 r_work: 0.4245 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13959 Z= 0.129 Angle : 0.618 13.380 18994 Z= 0.308 Chirality : 0.041 0.240 2207 Planarity : 0.004 0.044 2316 Dihedral : 13.068 140.872 2136 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Rotamer: Outliers : 1.85 % Allowed : 16.16 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1637 helix: 1.28 (0.17), residues: 972 sheet: -1.22 (0.45), residues: 130 loop : 0.09 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 324 HIS 0.007 0.001 HIS C 298 PHE 0.021 0.001 PHE A 443 TYR 0.016 0.001 TYR D 129 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 708) hydrogen bonds : angle 4.33790 ( 2069) covalent geometry : bond 0.00295 (13959) covalent geometry : angle 0.61806 (18994) *********************** 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 213 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4203 (mmp) cc_final: 0.3256 (mtp) REVERT: A 596 TYR cc_start: 0.6675 (p90) cc_final: 0.6398 (p90) REVERT: B 83 ASP cc_start: 0.5217 (m-30) cc_final: 0.3727 (p0) REVERT: B 119 MET cc_start: 0.6718 (mtt) cc_final: 0.6282 (mtm) REVERT: C 22 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6873 (mt-10) REVERT: E 101 MET cc_start: 0.4614 (ppp) cc_final: 0.3596 (ppp) REVERT: E 287 TYR cc_start: 0.7247 (m-80) cc_final: 0.6673 (m-80) outliers start: 27 outliers final: 23 residues processed: 201 average time/residue: 0.2349 time to fit residues: 71.8196 Evaluate side-chains 203 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 39 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU 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 217 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 246 LEU 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 145 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 36 optimal weight: 0.0670 chunk 140 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4638 r_free = 0.4638 target = 0.175903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.153939 restraints weight = 25528.731| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 3.14 r_work: 0.4216 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13959 Z= 0.137 Angle : 0.635 12.177 18994 Z= 0.316 Chirality : 0.043 0.332 2207 Planarity : 0.004 0.043 2316 Dihedral : 13.222 142.315 2136 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.92 % Allowed : 16.30 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1637 helix: 1.18 (0.17), residues: 977 sheet: -1.26 (0.45), residues: 130 loop : 0.06 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 324 HIS 0.006 0.001 HIS C 298 PHE 0.019 0.002 PHE A 346 TYR 0.017 0.001 TYR C 308 ARG 0.006 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 708) hydrogen bonds : angle 4.39490 ( 2069) covalent geometry : bond 0.00312 (13959) covalent geometry : angle 0.63494 (18994) *********************** 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 219 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4225 (mmp) cc_final: 0.3419 (mtt) REVERT: A 596 TYR cc_start: 0.6648 (p90) cc_final: 0.6401 (p90) REVERT: A 655 LYS cc_start: 0.7836 (mmmt) cc_final: 0.7428 (mmmm) REVERT: B 39 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: B 83 ASP cc_start: 0.5313 (m-30) cc_final: 0.3787 (p0) REVERT: B 119 MET cc_start: 0.6893 (mtt) cc_final: 0.6528 (mtm) REVERT: B 290 LYS cc_start: 0.7021 (ptpp) cc_final: 0.6739 (ptmt) REVERT: C 22 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6908 (mt-10) REVERT: E 101 MET cc_start: 0.4789 (ppp) cc_final: 0.3707 (ppp) REVERT: E 287 TYR cc_start: 0.7541 (m-80) cc_final: 0.6846 (m-80) outliers start: 28 outliers final: 26 residues processed: 208 average time/residue: 0.2367 time to fit residues: 74.0910 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 : 1.691 ------------------------------------------------------------------------------- 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 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU 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 217 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 246 LEU Chi-restraints excluded: chain E residue 307 LEU 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 75 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN C 12 ASN C 333 ASN E 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.176236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.155915 restraints weight = 25426.354| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.86 r_work: 0.4184 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13959 Z= 0.190 Angle : 0.707 11.027 18994 Z= 0.353 Chirality : 0.046 0.398 2207 Planarity : 0.005 0.044 2316 Dihedral : 13.536 147.798 2136 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.12 % Allowed : 16.58 % Favored : 81.30 % 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: 0.45 (0.21), residues: 1637 helix: 0.85 (0.17), residues: 984 sheet: -1.11 (0.48), residues: 116 loop : -0.20 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 324 HIS 0.009 0.002 HIS C 298 PHE 0.020 0.002 PHE A 346 TYR 0.019 0.002 TYR D 129 ARG 0.008 0.001 ARG B 285 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 708) hydrogen bonds : angle 4.62383 ( 2069) covalent geometry : bond 0.00441 (13959) covalent geometry : angle 0.70654 (18994) ********************** 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 208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4440 (mmp) cc_final: 0.3694 (mtt) REVERT: B 39 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: B 83 ASP cc_start: 0.5374 (m-30) cc_final: 0.3942 (p0) REVERT: B 119 MET cc_start: 0.6873 (mtt) cc_final: 0.6499 (mtm) REVERT: B 290 LYS cc_start: 0.7036 (ptpp) cc_final: 0.6814 (ptmt) REVERT: C 22 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6978 (mt-10) REVERT: D 245 LEU cc_start: 0.6760 (mm) cc_final: 0.6375 (pt) REVERT: E 101 MET cc_start: 0.4884 (ppp) cc_final: 0.3732 (ppp) outliers start: 31 outliers final: 27 residues processed: 197 average time/residue: 0.3127 time to fit residues: 94.0119 Evaluate side-chains 194 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 199 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 217 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 246 LEU Chi-restraints excluded: chain E residue 307 LEU 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 71 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN B 276 ASN D 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.169067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.147408 restraints weight = 26022.177| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 3.03 r_work: 0.4136 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13959 Z= 0.208 Angle : 0.728 10.458 18994 Z= 0.366 Chirality : 0.047 0.437 2207 Planarity : 0.005 0.050 2316 Dihedral : 13.784 148.669 2136 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.26 % Allowed : 17.19 % Favored : 80.55 % 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: 0.04 (0.21), residues: 1637 helix: 0.53 (0.16), residues: 990 sheet: -1.00 (0.49), residues: 109 loop : -0.49 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 324 HIS 0.008 0.002 HIS C 298 PHE 0.021 0.002 PHE A 443 TYR 0.035 0.002 TYR A 651 ARG 0.006 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 708) hydrogen bonds : angle 4.78172 ( 2069) covalent geometry : bond 0.00482 (13959) covalent geometry : angle 0.72797 (18994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7405.24 seconds wall clock time: 132 minutes 47.79 seconds (7967.79 seconds total)