Starting phenix.real_space_refine on Sun Aug 24 14:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvn_20494/08_2025/6pvn_20494.map" } resolution = 4.07 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13560 2.51 5 N 3464 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5218 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 626} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.99, per 1000 atoms: 0.19 Number of scatterers: 20874 At special positions: 0 Unit cell: (143.1, 143.1, 129.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3724 8.00 N 3464 7.00 C 13560 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: 1.42 Conformation dependent library (CDL) restraints added in 878.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 57.9% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.609A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 535 removed outlier: 3.566A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 554 " --> pdb=" O CYS A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 565 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 149 removed outlier: 3.640A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.525A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.542A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 459 removed outlier: 3.687A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 505 removed outlier: 3.524A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 554 " --> pdb=" O CYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 565 Processing helix chain 'B' and resid 570 through 576 removed outlier: 3.808A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 586 through 610 removed outlier: 3.852A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 634 removed outlier: 4.005A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.802A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.670A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.903A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 3.668A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.937A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 436 " --> pdb=" O LYS C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.925A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 554 " --> pdb=" O CYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 565 Processing helix chain 'C' and resid 570 through 576 removed outlier: 3.810A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 586 Processing helix chain 'C' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 132 through 149 removed outlier: 3.639A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.605A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.858A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.526A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.709A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.518A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.803A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.669A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.543A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.904A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 removed outlier: 3.667A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.608A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.723A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.592A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.936A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 459 removed outlier: 3.688A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 505 removed outlier: 3.523A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 501 " --> pdb=" O ILE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 535 removed outlier: 3.565A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.926A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 554 " --> pdb=" O CYS D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 565 Processing helix chain 'D' and resid 570 through 576 removed outlier: 3.809A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 586 through 610 removed outlier: 3.853A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 634 removed outlier: 4.006A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 665 removed outlier: 3.958A pdb=" N PHE D 656 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 681 removed outlier: 3.875A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 704 removed outlier: 3.763A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA2, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'D' and resid 387 through 388 764 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6542 1.34 - 1.46: 5002 1.46 - 1.58: 9576 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 21324 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.80e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.66e+00 bond pdb=" C ASP D 752 " pdb=" N PRO D 753 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.25e-02 6.40e+03 6.44e+00 ... (remaining 21319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 27590 2.87 - 5.74: 1090 5.74 - 8.60: 140 8.60 - 11.47: 48 11.47 - 14.34: 4 Bond angle restraints: 28872 Sorted by residual: angle pdb=" N ILE B 652 " pdb=" CA ILE B 652 " pdb=" C ILE B 652 " ideal model delta sigma weight residual 112.29 105.14 7.15 9.40e-01 1.13e+00 5.78e+01 angle pdb=" N ILE A 652 " pdb=" CA ILE A 652 " pdb=" C ILE A 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE C 652 " pdb=" CA ILE C 652 " pdb=" C ILE C 652 " ideal model delta sigma weight residual 112.29 105.19 7.10 9.40e-01 1.13e+00 5.70e+01 angle pdb=" N ILE D 652 " pdb=" CA ILE D 652 " pdb=" C ILE D 652 " ideal model delta sigma weight residual 112.29 105.22 7.07 9.40e-01 1.13e+00 5.65e+01 angle pdb=" N LYS D 686 " pdb=" CA LYS D 686 " pdb=" C LYS D 686 " ideal model delta sigma weight residual 114.39 105.24 9.15 1.45e+00 4.76e-01 3.98e+01 ... (remaining 28867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 11599 15.63 - 31.27: 853 31.27 - 46.90: 244 46.90 - 62.54: 28 62.54 - 78.17: 28 Dihedral angle restraints: 12752 sinusoidal: 5152 harmonic: 7600 Sorted by residual: dihedral pdb=" CA SER A 648 " pdb=" C SER A 648 " pdb=" N THR A 649 " pdb=" CA THR A 649 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.37e+01 dihedral pdb=" CA SER D 648 " pdb=" C SER D 648 " pdb=" N THR D 649 " pdb=" CA THR D 649 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 dihedral pdb=" CA SER B 648 " pdb=" C SER B 648 " pdb=" N THR B 649 " pdb=" CA THR B 649 " ideal model delta harmonic sigma weight residual -180.00 -131.66 -48.34 0 5.00e+00 4.00e-02 9.35e+01 ... (remaining 12749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2310 0.051 - 0.103: 710 0.103 - 0.154: 190 0.154 - 0.205: 74 0.205 - 0.257: 24 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CB THR D 740 " pdb=" CA THR D 740 " pdb=" OG1 THR D 740 " pdb=" CG2 THR D 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB THR C 740 " pdb=" CA THR C 740 " pdb=" OG1 THR C 740 " pdb=" CG2 THR C 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 740 " pdb=" CA THR A 740 " pdb=" OG1 THR A 740 " pdb=" CG2 THR A 740 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3305 not shown) Planarity restraints: 3608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 754 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 755 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 754 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO A 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 755 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 754 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.71e+00 pdb=" N PRO D 755 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " -0.042 5.00e-02 4.00e+02 ... (remaining 3605 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 5115 2.78 - 3.31: 19004 3.31 - 3.84: 31607 3.84 - 4.37: 36282 4.37 - 4.90: 61241 Nonbonded interactions: 153249 Sorted by model distance: nonbonded pdb=" NH2 ARG C 464 " pdb=" O GLU C 467 " model vdw 2.256 3.120 nonbonded pdb=" NH2 ARG A 464 " pdb=" O GLU A 467 " model vdw 2.256 3.120 nonbonded pdb=" NH2 ARG B 464 " pdb=" O GLU B 467 " model vdw 2.256 3.120 nonbonded pdb=" NH2 ARG D 464 " pdb=" O GLU D 467 " model vdw 2.256 3.120 nonbonded pdb=" OE2 GLU A 751 " pdb=" NZ LYS B 174 " model vdw 2.298 3.120 ... (remaining 153244 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.006 0.065 21324 Z= 0.297 Angle : 1.328 14.338 28872 Z= 0.769 Chirality : 0.060 0.257 3308 Planarity : 0.007 0.078 3608 Dihedral : 12.870 78.173 7816 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.21 % Favored : 85.32 % Rotamer: Outliers : 1.23 % Allowed : 8.11 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.84 (0.09), residues: 2568 helix: -4.54 (0.06), residues: 1420 sheet: None (None), residues: 0 loop : -4.50 (0.13), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 464 TYR 0.036 0.002 TYR D 213 PHE 0.043 0.003 PHE D 542 TRP 0.026 0.002 TRP C 692 HIS 0.012 0.002 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00613 (21324) covalent geometry : angle 1.32808 (28872) hydrogen bonds : bond 0.33380 ( 764) hydrogen bonds : angle 10.39934 ( 2244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 848 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.7882 (tpp) cc_final: 0.7550 (tpp) REVERT: A 335 THR cc_start: 0.9343 (p) cc_final: 0.9078 (t) REVERT: A 353 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8545 (mmtm) REVERT: A 397 THR cc_start: 0.8472 (m) cc_final: 0.8127 (p) REVERT: A 438 LYS cc_start: 0.8236 (tttp) cc_final: 0.8011 (ttpp) REVERT: A 479 MET cc_start: 0.0779 (mmm) cc_final: 0.0305 (mtm) REVERT: A 540 TYR cc_start: 0.6049 (t80) cc_final: 0.5804 (t80) REVERT: A 584 LEU cc_start: 0.8308 (tm) cc_final: 0.8043 (tt) REVERT: A 677 MET cc_start: 0.8402 (mtt) cc_final: 0.8048 (mtt) REVERT: A 687 GLU cc_start: 0.7629 (tp30) cc_final: 0.7386 (pp20) REVERT: A 734 ILE cc_start: 0.7687 (mt) cc_final: 0.7368 (mm) REVERT: A 748 PHE cc_start: 0.7359 (p90) cc_final: 0.6786 (p90) REVERT: B 159 MET cc_start: 0.7754 (tpp) cc_final: 0.6867 (tpp) REVERT: B 250 PHE cc_start: 0.7777 (p90) cc_final: 0.7547 (p90) REVERT: B 251 ASN cc_start: 0.5207 (t0) cc_final: 0.4891 (t0) REVERT: B 282 MET cc_start: 0.8352 (mmm) cc_final: 0.8012 (mmt) REVERT: B 335 THR cc_start: 0.9306 (p) cc_final: 0.9020 (t) REVERT: B 479 MET cc_start: 0.0663 (mmm) cc_final: 0.0182 (mtm) REVERT: B 497 ILE cc_start: 0.9165 (tp) cc_final: 0.8828 (tt) REVERT: B 661 TYR cc_start: 0.9453 (t80) cc_final: 0.8548 (t80) REVERT: B 677 MET cc_start: 0.8290 (mtt) cc_final: 0.7824 (mtt) REVERT: B 722 LYS cc_start: 0.6287 (ttmt) cc_final: 0.6038 (ttmt) REVERT: B 734 ILE cc_start: 0.7914 (mt) cc_final: 0.7587 (mm) REVERT: B 748 PHE cc_start: 0.7556 (p90) cc_final: 0.7045 (p90) REVERT: C 159 MET cc_start: 0.7880 (tpp) cc_final: 0.7560 (tpp) REVERT: C 335 THR cc_start: 0.9344 (p) cc_final: 0.9117 (t) REVERT: C 353 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8509 (mmtm) REVERT: C 397 THR cc_start: 0.8462 (m) cc_final: 0.8123 (p) REVERT: C 438 LYS cc_start: 0.8211 (tttp) cc_final: 0.7997 (ttpp) REVERT: C 479 MET cc_start: 0.0804 (mmm) cc_final: 0.0325 (mtm) REVERT: C 540 TYR cc_start: 0.6072 (t80) cc_final: 0.5828 (t80) REVERT: C 584 LEU cc_start: 0.8317 (tm) cc_final: 0.8021 (tt) REVERT: C 605 LEU cc_start: 0.9091 (mp) cc_final: 0.8871 (mt) REVERT: C 677 MET cc_start: 0.8332 (mtt) cc_final: 0.7990 (mtt) REVERT: C 687 GLU cc_start: 0.7591 (tp30) cc_final: 0.7355 (pp20) REVERT: C 734 ILE cc_start: 0.7683 (mt) cc_final: 0.7349 (mm) REVERT: C 748 PHE cc_start: 0.7428 (p90) cc_final: 0.7005 (p90) REVERT: D 159 MET cc_start: 0.7876 (tpp) cc_final: 0.7537 (tpp) REVERT: D 335 THR cc_start: 0.9339 (p) cc_final: 0.9110 (t) REVERT: D 353 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8501 (mmtm) REVERT: D 397 THR cc_start: 0.8468 (m) cc_final: 0.8116 (p) REVERT: D 438 LYS cc_start: 0.8215 (tttp) cc_final: 0.8005 (ttpp) REVERT: D 479 MET cc_start: 0.0774 (mmm) cc_final: 0.0304 (mtm) REVERT: D 540 TYR cc_start: 0.6091 (t80) cc_final: 0.5837 (t80) REVERT: D 584 LEU cc_start: 0.8311 (tm) cc_final: 0.8016 (tt) REVERT: D 605 LEU cc_start: 0.9087 (mp) cc_final: 0.8880 (mt) REVERT: D 677 MET cc_start: 0.8340 (mtt) cc_final: 0.7998 (mtt) REVERT: D 687 GLU cc_start: 0.7577 (tp30) cc_final: 0.7352 (pp20) REVERT: D 734 ILE cc_start: 0.7690 (mt) cc_final: 0.7307 (mm) REVERT: D 748 PHE cc_start: 0.7396 (p90) cc_final: 0.6945 (p90) outliers start: 28 outliers final: 8 residues processed: 868 average time/residue: 0.1333 time to fit residues: 181.0746 Evaluate side-chains 490 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 482 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 HIS A 426 HIS A 483 GLN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 426 HIS B 483 GLN B 585 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 HIS C 426 HIS C 483 GLN C 570 GLN C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 HIS D 426 HIS D 483 GLN D 585 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115819 restraints weight = 35339.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118294 restraints weight = 23327.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120110 restraints weight = 17988.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.120828 restraints weight = 15118.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121492 restraints weight = 13748.595| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21324 Z= 0.175 Angle : 0.848 13.365 28872 Z= 0.440 Chirality : 0.046 0.219 3308 Planarity : 0.006 0.079 3608 Dihedral : 7.727 42.655 2804 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.17 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.73 (0.13), residues: 2568 helix: -2.37 (0.11), residues: 1404 sheet: -4.86 (0.36), residues: 40 loop : -4.12 (0.14), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 464 TYR 0.019 0.002 TYR A 213 PHE 0.025 0.002 PHE A 250 TRP 0.015 0.002 TRP D 739 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00363 (21324) covalent geometry : angle 0.84771 (28872) hydrogen bonds : bond 0.05891 ( 764) hydrogen bonds : angle 5.18439 ( 2244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8474 (mtpt) REVERT: A 129 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 159 MET cc_start: 0.7846 (tpp) cc_final: 0.6691 (tpp) REVERT: A 163 THR cc_start: 0.8585 (m) cc_final: 0.8361 (p) REVERT: A 216 GLN cc_start: 0.8794 (tt0) cc_final: 0.8421 (mt0) REVERT: A 221 ILE cc_start: 0.9594 (mt) cc_final: 0.9333 (mm) REVERT: A 248 VAL cc_start: 0.8111 (m) cc_final: 0.7907 (p) REVERT: A 297 ASN cc_start: 0.7697 (m-40) cc_final: 0.6982 (m110) REVERT: A 335 THR cc_start: 0.9272 (p) cc_final: 0.8910 (t) REVERT: A 353 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8405 (mmtp) REVERT: A 479 MET cc_start: 0.0596 (mmm) cc_final: 0.0305 (mtm) REVERT: A 498 SER cc_start: 0.8954 (t) cc_final: 0.8649 (p) REVERT: A 540 TYR cc_start: 0.6031 (t80) cc_final: 0.5777 (t80) REVERT: A 555 MET cc_start: 0.8648 (ttm) cc_final: 0.8407 (ttm) REVERT: A 627 ASP cc_start: 0.7424 (t70) cc_final: 0.7199 (t70) REVERT: A 659 ILE cc_start: 0.8955 (pt) cc_final: 0.8696 (mm) REVERT: A 677 MET cc_start: 0.7735 (mtt) cc_final: 0.7468 (mtt) REVERT: A 748 PHE cc_start: 0.7508 (p90) cc_final: 0.7196 (p90) REVERT: B 121 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8422 (mtpt) REVERT: B 159 MET cc_start: 0.7680 (tpp) cc_final: 0.6530 (tpp) REVERT: B 248 VAL cc_start: 0.8147 (m) cc_final: 0.7913 (p) REVERT: B 260 TYR cc_start: 0.8804 (t80) cc_final: 0.8558 (t80) REVERT: B 282 MET cc_start: 0.8184 (mmm) cc_final: 0.7762 (mmt) REVERT: B 297 ASN cc_start: 0.7880 (m-40) cc_final: 0.7440 (m110) REVERT: B 335 THR cc_start: 0.9256 (p) cc_final: 0.8827 (t) REVERT: B 464 ARG cc_start: 0.6065 (tpm170) cc_final: 0.5767 (mmt-90) REVERT: B 479 MET cc_start: 0.1079 (mmm) cc_final: 0.0581 (mtm) REVERT: B 497 ILE cc_start: 0.9206 (tp) cc_final: 0.9005 (mt) REVERT: B 534 ILE cc_start: 0.9248 (tp) cc_final: 0.9044 (tp) REVERT: B 555 MET cc_start: 0.8733 (ttm) cc_final: 0.8447 (ttm) REVERT: B 569 PHE cc_start: 0.8037 (m-10) cc_final: 0.7824 (m-10) REVERT: B 677 MET cc_start: 0.7619 (mtt) cc_final: 0.7275 (mtt) REVERT: B 687 GLU cc_start: 0.8250 (pp20) cc_final: 0.7544 (pp20) REVERT: B 748 PHE cc_start: 0.7517 (p90) cc_final: 0.7287 (p90) REVERT: C 121 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8489 (mtpt) REVERT: C 129 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 159 MET cc_start: 0.7874 (tpp) cc_final: 0.6727 (tpp) REVERT: C 163 THR cc_start: 0.8543 (m) cc_final: 0.8315 (p) REVERT: C 216 GLN cc_start: 0.8792 (tt0) cc_final: 0.8421 (mt0) REVERT: C 221 ILE cc_start: 0.9619 (mt) cc_final: 0.9385 (mm) REVERT: C 248 VAL cc_start: 0.8117 (m) cc_final: 0.7907 (p) REVERT: C 297 ASN cc_start: 0.7726 (m-40) cc_final: 0.6871 (m-40) REVERT: C 335 THR cc_start: 0.9270 (p) cc_final: 0.8902 (t) REVERT: C 353 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8490 (mmtm) REVERT: C 445 PHE cc_start: 0.9034 (t80) cc_final: 0.8751 (t80) REVERT: C 479 MET cc_start: 0.0589 (mmm) cc_final: 0.0300 (mtm) REVERT: C 498 SER cc_start: 0.8956 (t) cc_final: 0.8636 (p) REVERT: C 513 LEU cc_start: 0.8081 (mt) cc_final: 0.7858 (mt) REVERT: C 540 TYR cc_start: 0.6145 (t80) cc_final: 0.5873 (t80) REVERT: C 605 LEU cc_start: 0.9098 (mp) cc_final: 0.8522 (mt) REVERT: C 627 ASP cc_start: 0.7391 (t70) cc_final: 0.7172 (t70) REVERT: C 659 ILE cc_start: 0.8960 (pt) cc_final: 0.8703 (mm) REVERT: C 677 MET cc_start: 0.7703 (mtt) cc_final: 0.7471 (mtt) REVERT: C 748 PHE cc_start: 0.7532 (p90) cc_final: 0.7112 (p90) REVERT: D 121 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8477 (mtpt) REVERT: D 129 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7403 (tm-30) REVERT: D 159 MET cc_start: 0.7855 (tpp) cc_final: 0.6698 (tpp) REVERT: D 163 THR cc_start: 0.8574 (m) cc_final: 0.8352 (p) REVERT: D 216 GLN cc_start: 0.8810 (tt0) cc_final: 0.8435 (mt0) REVERT: D 221 ILE cc_start: 0.9600 (mt) cc_final: 0.9338 (mm) REVERT: D 248 VAL cc_start: 0.8115 (m) cc_final: 0.7901 (p) REVERT: D 297 ASN cc_start: 0.7705 (m-40) cc_final: 0.6993 (m110) REVERT: D 335 THR cc_start: 0.9272 (p) cc_final: 0.8909 (t) REVERT: D 353 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8398 (mmtp) REVERT: D 479 MET cc_start: 0.0590 (mmm) cc_final: 0.0302 (mtm) REVERT: D 498 SER cc_start: 0.8955 (t) cc_final: 0.8643 (p) REVERT: D 540 TYR cc_start: 0.6073 (t80) cc_final: 0.5812 (t80) REVERT: D 605 LEU cc_start: 0.9087 (mp) cc_final: 0.8538 (mt) REVERT: D 627 ASP cc_start: 0.7421 (t70) cc_final: 0.7196 (t70) REVERT: D 659 ILE cc_start: 0.8966 (pt) cc_final: 0.8721 (mm) REVERT: D 677 MET cc_start: 0.7773 (mtt) cc_final: 0.7526 (mtt) REVERT: D 734 ILE cc_start: 0.7332 (mt) cc_final: 0.6367 (tt) REVERT: D 748 PHE cc_start: 0.7520 (p90) cc_final: 0.7113 (p90) outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.1460 time to fit residues: 162.2676 Evaluate side-chains 493 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 195 optimal weight: 0.0270 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 234 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 256 HIS A 523 HIS A 570 GLN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS B 570 GLN B 585 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 523 HIS C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 523 HIS D 570 GLN D 585 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.146373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.116787 restraints weight = 35516.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119368 restraints weight = 23201.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120725 restraints weight = 17709.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121925 restraints weight = 15058.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122444 restraints weight = 13599.472| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21324 Z= 0.139 Angle : 0.763 11.966 28872 Z= 0.395 Chirality : 0.044 0.276 3308 Planarity : 0.005 0.070 3608 Dihedral : 6.967 36.587 2804 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.56 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.14), residues: 2568 helix: -1.45 (0.12), residues: 1460 sheet: -4.87 (0.35), residues: 40 loop : -4.23 (0.14), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 464 TYR 0.019 0.002 TYR D 208 PHE 0.025 0.001 PHE A 250 TRP 0.015 0.001 TRP B 493 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00291 (21324) covalent geometry : angle 0.76313 (28872) hydrogen bonds : bond 0.04166 ( 764) hydrogen bonds : angle 4.51974 ( 2244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8298 (mm) cc_final: 0.8018 (mt) REVERT: A 121 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8486 (mtpt) REVERT: A 159 MET cc_start: 0.7647 (tpp) cc_final: 0.7344 (tpp) REVERT: A 216 GLN cc_start: 0.8803 (tt0) cc_final: 0.8440 (mt0) REVERT: A 221 ILE cc_start: 0.9604 (mt) cc_final: 0.9381 (mm) REVERT: A 249 PHE cc_start: 0.6291 (p90) cc_final: 0.4200 (m-80) REVERT: A 297 ASN cc_start: 0.7723 (m-40) cc_final: 0.7443 (m110) REVERT: A 335 THR cc_start: 0.9286 (p) cc_final: 0.8947 (t) REVERT: A 353 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8442 (mmtm) REVERT: A 498 SER cc_start: 0.8916 (t) cc_final: 0.8637 (p) REVERT: A 540 TYR cc_start: 0.6220 (t80) cc_final: 0.5927 (t80) REVERT: A 555 MET cc_start: 0.8549 (ttm) cc_final: 0.8313 (ttm) REVERT: A 569 PHE cc_start: 0.8021 (m-80) cc_final: 0.7781 (m-10) REVERT: A 605 LEU cc_start: 0.9222 (mt) cc_final: 0.9016 (mm) REVERT: A 659 ILE cc_start: 0.8869 (pt) cc_final: 0.8646 (mm) REVERT: A 677 MET cc_start: 0.7825 (mtt) cc_final: 0.7532 (mtt) REVERT: A 685 SER cc_start: 0.9173 (t) cc_final: 0.8862 (t) REVERT: A 748 PHE cc_start: 0.7489 (p90) cc_final: 0.7218 (p90) REVERT: B 121 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8455 (mtpt) REVERT: B 159 MET cc_start: 0.7423 (tpp) cc_final: 0.6708 (tpp) REVERT: B 248 VAL cc_start: 0.8177 (m) cc_final: 0.7969 (p) REVERT: B 297 ASN cc_start: 0.7875 (m-40) cc_final: 0.7329 (m110) REVERT: B 327 ARG cc_start: 0.7016 (tpt170) cc_final: 0.6783 (tpt170) REVERT: B 335 THR cc_start: 0.9240 (p) cc_final: 0.8758 (t) REVERT: B 464 ARG cc_start: 0.6161 (tpm170) cc_final: 0.5949 (mmt-90) REVERT: B 497 ILE cc_start: 0.9230 (tp) cc_final: 0.8914 (tt) REVERT: B 555 MET cc_start: 0.8689 (ttm) cc_final: 0.8459 (ttm) REVERT: B 605 LEU cc_start: 0.8906 (mp) cc_final: 0.8454 (mt) REVERT: B 677 MET cc_start: 0.7645 (mtt) cc_final: 0.7339 (mtt) REVERT: B 679 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7659 (tp30) REVERT: C 119 LEU cc_start: 0.8277 (mm) cc_final: 0.8006 (mt) REVERT: C 121 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8496 (mtpt) REVERT: C 159 MET cc_start: 0.7685 (tpp) cc_final: 0.7379 (tpp) REVERT: C 216 GLN cc_start: 0.8792 (tt0) cc_final: 0.8427 (mt0) REVERT: C 221 ILE cc_start: 0.9626 (mt) cc_final: 0.9402 (mm) REVERT: C 249 PHE cc_start: 0.6317 (p90) cc_final: 0.4233 (m-80) REVERT: C 297 ASN cc_start: 0.7749 (m-40) cc_final: 0.7421 (m110) REVERT: C 335 THR cc_start: 0.9271 (p) cc_final: 0.8937 (t) REVERT: C 353 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8414 (mmtm) REVERT: C 445 PHE cc_start: 0.9068 (t80) cc_final: 0.8849 (t80) REVERT: C 498 SER cc_start: 0.8925 (t) cc_final: 0.8646 (p) REVERT: C 540 TYR cc_start: 0.6220 (t80) cc_final: 0.5927 (t80) REVERT: C 555 MET cc_start: 0.8539 (ttm) cc_final: 0.8296 (ttm) REVERT: C 569 PHE cc_start: 0.8029 (m-80) cc_final: 0.7791 (m-10) REVERT: C 605 LEU cc_start: 0.9039 (mp) cc_final: 0.8557 (mt) REVERT: C 659 ILE cc_start: 0.8878 (pt) cc_final: 0.8676 (mm) REVERT: C 677 MET cc_start: 0.7761 (mtt) cc_final: 0.7474 (mtt) REVERT: C 685 SER cc_start: 0.9168 (t) cc_final: 0.8960 (t) REVERT: D 119 LEU cc_start: 0.8284 (mm) cc_final: 0.8008 (mt) REVERT: D 121 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8504 (mtpt) REVERT: D 129 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7281 (tm-30) REVERT: D 159 MET cc_start: 0.7659 (tpp) cc_final: 0.7342 (tpp) REVERT: D 216 GLN cc_start: 0.8812 (tt0) cc_final: 0.8452 (mt0) REVERT: D 221 ILE cc_start: 0.9603 (mt) cc_final: 0.9372 (mm) REVERT: D 249 PHE cc_start: 0.6326 (p90) cc_final: 0.4221 (m-80) REVERT: D 297 ASN cc_start: 0.7757 (m-40) cc_final: 0.7454 (m110) REVERT: D 335 THR cc_start: 0.9282 (p) cc_final: 0.8954 (t) REVERT: D 353 LYS cc_start: 0.9113 (mmtt) cc_final: 0.7880 (mmtp) REVERT: D 498 SER cc_start: 0.8933 (t) cc_final: 0.8652 (p) REVERT: D 540 TYR cc_start: 0.6267 (t80) cc_final: 0.5968 (t80) REVERT: D 555 MET cc_start: 0.8531 (ttm) cc_final: 0.8291 (ttm) REVERT: D 569 PHE cc_start: 0.8037 (m-80) cc_final: 0.7797 (m-10) REVERT: D 605 LEU cc_start: 0.9045 (mp) cc_final: 0.8565 (mt) REVERT: D 659 ILE cc_start: 0.8868 (pt) cc_final: 0.8655 (mm) REVERT: D 677 MET cc_start: 0.7804 (mtt) cc_final: 0.7485 (mtt) outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.1340 time to fit residues: 140.8448 Evaluate side-chains 460 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 460 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 119 optimal weight: 0.4980 chunk 247 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN D 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.145733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116114 restraints weight = 35745.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118639 restraints weight = 23908.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119848 restraints weight = 18462.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121185 restraints weight = 15851.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121683 restraints weight = 14236.092| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21324 Z= 0.136 Angle : 0.737 9.951 28872 Z= 0.386 Chirality : 0.044 0.302 3308 Planarity : 0.005 0.080 3608 Dihedral : 6.574 37.068 2804 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.25 % Favored : 85.59 % Rotamer: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.15), residues: 2568 helix: -0.99 (0.13), residues: 1484 sheet: -4.80 (0.33), residues: 60 loop : -4.26 (0.15), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 464 TYR 0.018 0.001 TYR B 260 PHE 0.026 0.001 PHE A 250 TRP 0.016 0.001 TRP B 493 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00292 (21324) covalent geometry : angle 0.73730 (28872) hydrogen bonds : bond 0.03511 ( 764) hydrogen bonds : angle 4.34395 ( 2244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 618 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8505 (mm) cc_final: 0.8216 (mt) REVERT: A 121 LYS cc_start: 0.8910 (mmmt) cc_final: 0.8474 (mtpt) REVERT: A 159 MET cc_start: 0.7596 (tpp) cc_final: 0.7268 (tpp) REVERT: A 216 GLN cc_start: 0.8835 (tt0) cc_final: 0.8366 (mt0) REVERT: A 249 PHE cc_start: 0.6323 (p90) cc_final: 0.4178 (m-80) REVERT: A 297 ASN cc_start: 0.7971 (m-40) cc_final: 0.7462 (m110) REVERT: A 335 THR cc_start: 0.9289 (p) cc_final: 0.8922 (t) REVERT: A 353 LYS cc_start: 0.9083 (mmtt) cc_final: 0.7995 (mmtp) REVERT: A 479 MET cc_start: -0.0737 (mmm) cc_final: -0.0954 (mmm) REVERT: A 540 TYR cc_start: 0.6342 (t80) cc_final: 0.6014 (t80) REVERT: A 555 MET cc_start: 0.8552 (ttm) cc_final: 0.8298 (ttm) REVERT: A 569 PHE cc_start: 0.8054 (m-80) cc_final: 0.7806 (m-10) REVERT: A 659 ILE cc_start: 0.8908 (pt) cc_final: 0.8607 (mm) REVERT: A 677 MET cc_start: 0.7825 (mtt) cc_final: 0.7541 (mtt) REVERT: A 687 GLU cc_start: 0.7894 (pt0) cc_final: 0.7378 (pp20) REVERT: A 722 LYS cc_start: 0.6649 (tttt) cc_final: 0.6262 (tttt) REVERT: A 748 PHE cc_start: 0.7575 (p90) cc_final: 0.7296 (p90) REVERT: B 121 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8434 (mtpt) REVERT: B 159 MET cc_start: 0.7462 (tpp) cc_final: 0.6868 (tpp) REVERT: B 249 PHE cc_start: 0.5839 (p90) cc_final: 0.3604 (m-80) REVERT: B 335 THR cc_start: 0.9203 (p) cc_final: 0.8719 (t) REVERT: B 497 ILE cc_start: 0.9216 (tp) cc_final: 0.8941 (tt) REVERT: B 555 MET cc_start: 0.8680 (ttm) cc_final: 0.8436 (ttm) REVERT: B 569 PHE cc_start: 0.8023 (m-80) cc_final: 0.7754 (m-10) REVERT: B 605 LEU cc_start: 0.8901 (mp) cc_final: 0.8551 (mt) REVERT: B 677 MET cc_start: 0.7663 (mtt) cc_final: 0.7392 (mtt) REVERT: B 679 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7662 (tp30) REVERT: C 119 LEU cc_start: 0.8491 (mm) cc_final: 0.8225 (mt) REVERT: C 121 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8497 (mtpt) REVERT: C 129 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 159 MET cc_start: 0.7636 (tpp) cc_final: 0.7346 (tpp) REVERT: C 216 GLN cc_start: 0.8822 (tt0) cc_final: 0.8362 (mt0) REVERT: C 249 PHE cc_start: 0.6372 (p90) cc_final: 0.4268 (m-80) REVERT: C 297 ASN cc_start: 0.7998 (m-40) cc_final: 0.7435 (m110) REVERT: C 335 THR cc_start: 0.9269 (p) cc_final: 0.8909 (t) REVERT: C 353 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8476 (mmtm) REVERT: C 479 MET cc_start: -0.0757 (mmm) cc_final: -0.0977 (mmm) REVERT: C 540 TYR cc_start: 0.6364 (t80) cc_final: 0.6029 (t80) REVERT: C 569 PHE cc_start: 0.8172 (m-80) cc_final: 0.7935 (m-10) REVERT: C 605 LEU cc_start: 0.9045 (mp) cc_final: 0.8595 (mt) REVERT: C 659 ILE cc_start: 0.8931 (pt) cc_final: 0.8640 (mm) REVERT: C 687 GLU cc_start: 0.7922 (pt0) cc_final: 0.7384 (pp20) REVERT: C 722 LYS cc_start: 0.6631 (tttt) cc_final: 0.6268 (tttt) REVERT: D 119 LEU cc_start: 0.8509 (mm) cc_final: 0.8217 (mt) REVERT: D 121 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8488 (mtpt) REVERT: D 129 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7257 (tm-30) REVERT: D 159 MET cc_start: 0.7599 (tpp) cc_final: 0.7271 (tpp) REVERT: D 216 GLN cc_start: 0.8854 (tt0) cc_final: 0.8393 (mt0) REVERT: D 249 PHE cc_start: 0.6357 (p90) cc_final: 0.4220 (m-80) REVERT: D 297 ASN cc_start: 0.7985 (m-40) cc_final: 0.7488 (m110) REVERT: D 335 THR cc_start: 0.9281 (p) cc_final: 0.8930 (t) REVERT: D 353 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8470 (mmtm) REVERT: D 479 MET cc_start: -0.0736 (mmm) cc_final: -0.0972 (mmm) REVERT: D 540 TYR cc_start: 0.6390 (t80) cc_final: 0.6050 (t80) REVERT: D 569 PHE cc_start: 0.8070 (m-80) cc_final: 0.7836 (m-10) REVERT: D 605 LEU cc_start: 0.9031 (mp) cc_final: 0.8617 (mt) REVERT: D 659 ILE cc_start: 0.8918 (pt) cc_final: 0.8633 (mm) REVERT: D 677 MET cc_start: 0.7795 (mtt) cc_final: 0.7585 (mtt) REVERT: D 687 GLU cc_start: 0.7893 (pt0) cc_final: 0.7379 (pp20) REVERT: D 722 LYS cc_start: 0.6671 (tttt) cc_final: 0.5875 (tttt) outliers start: 2 outliers final: 0 residues processed: 620 average time/residue: 0.1376 time to fit residues: 137.1897 Evaluate side-chains 474 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 86 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 123 optimal weight: 0.0170 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 = 0.3696 r_free = 0.3696 target = 0.147113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117770 restraints weight = 35087.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120213 restraints weight = 23564.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121436 restraints weight = 18258.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122601 restraints weight = 15759.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123079 restraints weight = 14379.785| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21324 Z= 0.131 Angle : 0.730 12.136 28872 Z= 0.377 Chirality : 0.043 0.230 3308 Planarity : 0.005 0.081 3608 Dihedral : 6.263 37.437 2804 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.37 % Favored : 85.36 % Rotamer: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.15), residues: 2568 helix: -0.56 (0.13), residues: 1492 sheet: -4.48 (0.34), residues: 76 loop : -4.17 (0.15), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 464 TYR 0.042 0.002 TYR B 650 PHE 0.020 0.001 PHE A 249 TRP 0.021 0.001 TRP D 481 HIS 0.002 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00284 (21324) covalent geometry : angle 0.73032 (28872) hydrogen bonds : bond 0.03333 ( 764) hydrogen bonds : angle 4.24376 ( 2244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 612 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8580 (mm) cc_final: 0.8268 (mt) REVERT: A 121 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8451 (mtmt) REVERT: A 129 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 159 MET cc_start: 0.7672 (tpp) cc_final: 0.7352 (tpp) REVERT: A 249 PHE cc_start: 0.6072 (p90) cc_final: 0.4054 (m-80) REVERT: A 280 LEU cc_start: 0.9200 (tp) cc_final: 0.8996 (tp) REVERT: A 297 ASN cc_start: 0.7984 (m-40) cc_final: 0.7484 (m110) REVERT: A 335 THR cc_start: 0.9265 (p) cc_final: 0.8844 (t) REVERT: A 353 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8240 (mmtp) REVERT: A 540 TYR cc_start: 0.6417 (t80) cc_final: 0.6028 (t80) REVERT: A 555 MET cc_start: 0.8609 (ttm) cc_final: 0.8346 (ttm) REVERT: A 659 ILE cc_start: 0.8929 (pt) cc_final: 0.8579 (mm) REVERT: A 677 MET cc_start: 0.7776 (mtt) cc_final: 0.7496 (mtt) REVERT: A 685 SER cc_start: 0.9275 (t) cc_final: 0.9042 (t) REVERT: A 722 LYS cc_start: 0.6664 (tttt) cc_final: 0.6211 (tttt) REVERT: A 748 PHE cc_start: 0.7609 (p90) cc_final: 0.7351 (p90) REVERT: B 119 LEU cc_start: 0.8649 (mm) cc_final: 0.8358 (mt) REVERT: B 121 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8388 (mtpt) REVERT: B 131 CYS cc_start: 0.7687 (t) cc_final: 0.6080 (t) REVERT: B 159 MET cc_start: 0.7446 (tpp) cc_final: 0.6744 (tpp) REVERT: B 249 PHE cc_start: 0.5709 (p90) cc_final: 0.3761 (m-80) REVERT: B 297 ASN cc_start: 0.8103 (m110) cc_final: 0.7628 (m110) REVERT: B 320 MET cc_start: 0.8558 (mmm) cc_final: 0.8173 (mmm) REVERT: B 335 THR cc_start: 0.9188 (p) cc_final: 0.8724 (t) REVERT: B 351 MET cc_start: 0.8217 (mmm) cc_final: 0.7959 (mmm) REVERT: B 479 MET cc_start: -0.0723 (mmm) cc_final: -0.0926 (mmm) REVERT: B 500 LYS cc_start: 0.6500 (ttpt) cc_final: 0.6104 (tptt) REVERT: B 555 MET cc_start: 0.8614 (ttm) cc_final: 0.8388 (ttm) REVERT: B 562 MET cc_start: 0.8718 (ttt) cc_final: 0.8464 (ttt) REVERT: B 569 PHE cc_start: 0.8017 (m-80) cc_final: 0.7770 (m-10) REVERT: B 654 PHE cc_start: 0.8698 (t80) cc_final: 0.8491 (t80) REVERT: B 679 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7345 (tp30) REVERT: C 119 LEU cc_start: 0.8568 (mm) cc_final: 0.8280 (mt) REVERT: C 121 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8485 (mtpt) REVERT: C 129 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 159 MET cc_start: 0.7645 (tpp) cc_final: 0.7283 (tpp) REVERT: C 249 PHE cc_start: 0.6100 (p90) cc_final: 0.4204 (m-80) REVERT: C 268 LEU cc_start: 0.8929 (pp) cc_final: 0.8728 (pp) REVERT: C 297 ASN cc_start: 0.7910 (m-40) cc_final: 0.7472 (m110) REVERT: C 335 THR cc_start: 0.9247 (p) cc_final: 0.8827 (t) REVERT: C 353 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8302 (mmtp) REVERT: C 540 TYR cc_start: 0.6399 (t80) cc_final: 0.6014 (t80) REVERT: C 569 PHE cc_start: 0.8165 (m-80) cc_final: 0.7943 (m-10) REVERT: C 659 ILE cc_start: 0.8952 (pt) cc_final: 0.8610 (mm) REVERT: C 677 MET cc_start: 0.7515 (mtt) cc_final: 0.7287 (mtt) REVERT: C 722 LYS cc_start: 0.6690 (tttt) cc_final: 0.6210 (tttt) REVERT: D 119 LEU cc_start: 0.8574 (mm) cc_final: 0.8278 (mt) REVERT: D 129 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7226 (tm-30) REVERT: D 159 MET cc_start: 0.7619 (tpp) cc_final: 0.7279 (tpp) REVERT: D 249 PHE cc_start: 0.6065 (p90) cc_final: 0.4061 (m-80) REVERT: D 268 LEU cc_start: 0.8917 (pp) cc_final: 0.8715 (pp) REVERT: D 297 ASN cc_start: 0.7992 (m-40) cc_final: 0.7488 (m110) REVERT: D 335 THR cc_start: 0.9262 (p) cc_final: 0.8841 (t) REVERT: D 353 LYS cc_start: 0.9100 (mmtt) cc_final: 0.7950 (mmtp) REVERT: D 540 TYR cc_start: 0.6426 (t80) cc_final: 0.6043 (t80) REVERT: D 659 ILE cc_start: 0.8951 (pt) cc_final: 0.8602 (mm) REVERT: D 677 MET cc_start: 0.7765 (mtt) cc_final: 0.7552 (mtt) outliers start: 4 outliers final: 4 residues processed: 616 average time/residue: 0.1335 time to fit residues: 133.6082 Evaluate side-chains 442 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 438 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 8 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113669 restraints weight = 35244.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116189 restraints weight = 23512.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117415 restraints weight = 18118.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118394 restraints weight = 15512.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119467 restraints weight = 13968.252| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21324 Z= 0.173 Angle : 0.751 11.242 28872 Z= 0.390 Chirality : 0.046 0.397 3308 Planarity : 0.005 0.068 3608 Dihedral : 6.113 38.180 2804 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.25 % Favored : 85.59 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.16), residues: 2568 helix: -0.27 (0.13), residues: 1468 sheet: -4.55 (0.36), residues: 60 loop : -4.09 (0.15), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 733 TYR 0.021 0.002 TYR B 540 PHE 0.025 0.002 PHE A 249 TRP 0.017 0.001 TRP B 493 HIS 0.003 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00397 (21324) covalent geometry : angle 0.75114 (28872) hydrogen bonds : bond 0.03240 ( 764) hydrogen bonds : angle 4.27363 ( 2244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8534 (mm) cc_final: 0.8294 (mt) REVERT: A 159 MET cc_start: 0.7711 (tpp) cc_final: 0.6855 (tpp) REVERT: A 163 THR cc_start: 0.8625 (m) cc_final: 0.8396 (p) REVERT: A 249 PHE cc_start: 0.6358 (p90) cc_final: 0.4240 (m-80) REVERT: A 297 ASN cc_start: 0.8025 (m-40) cc_final: 0.7531 (m110) REVERT: A 335 THR cc_start: 0.9273 (p) cc_final: 0.8899 (t) REVERT: A 351 MET cc_start: 0.7996 (mmm) cc_final: 0.7592 (mmm) REVERT: A 353 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8096 (mmtp) REVERT: A 506 PHE cc_start: 0.7966 (t80) cc_final: 0.7730 (t80) REVERT: A 540 TYR cc_start: 0.6362 (t80) cc_final: 0.6032 (t80) REVERT: A 555 MET cc_start: 0.8673 (ttm) cc_final: 0.8462 (ttm) REVERT: A 627 ASP cc_start: 0.7453 (t70) cc_final: 0.7238 (t0) REVERT: A 659 ILE cc_start: 0.8948 (pt) cc_final: 0.8630 (mm) REVERT: A 677 MET cc_start: 0.7889 (mtt) cc_final: 0.7617 (mtt) REVERT: B 159 MET cc_start: 0.7476 (tpp) cc_final: 0.6820 (tpp) REVERT: B 249 PHE cc_start: 0.5878 (p90) cc_final: 0.3524 (m-80) REVERT: B 297 ASN cc_start: 0.8313 (m110) cc_final: 0.7711 (m110) REVERT: B 320 MET cc_start: 0.8722 (mmm) cc_final: 0.8328 (mmm) REVERT: B 335 THR cc_start: 0.9207 (p) cc_final: 0.8735 (t) REVERT: B 351 MET cc_start: 0.8371 (mmm) cc_final: 0.8064 (mmm) REVERT: B 555 MET cc_start: 0.8661 (ttm) cc_final: 0.8439 (ttm) REVERT: B 562 MET cc_start: 0.8794 (ttt) cc_final: 0.8547 (ttt) REVERT: B 569 PHE cc_start: 0.8153 (m-80) cc_final: 0.7857 (m-10) REVERT: B 679 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7486 (tp30) REVERT: C 119 LEU cc_start: 0.8516 (mm) cc_final: 0.8275 (mt) REVERT: C 129 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7515 (tm-30) REVERT: C 159 MET cc_start: 0.7683 (tpp) cc_final: 0.7373 (tpp) REVERT: C 249 PHE cc_start: 0.6474 (p90) cc_final: 0.4210 (m-80) REVERT: C 297 ASN cc_start: 0.8002 (m-40) cc_final: 0.7506 (m110) REVERT: C 335 THR cc_start: 0.9254 (p) cc_final: 0.8879 (t) REVERT: C 351 MET cc_start: 0.8017 (mmm) cc_final: 0.7625 (mmm) REVERT: C 353 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8108 (mmtp) REVERT: C 506 PHE cc_start: 0.7967 (t80) cc_final: 0.7742 (t80) REVERT: C 540 TYR cc_start: 0.6372 (t80) cc_final: 0.6038 (t80) REVERT: C 569 PHE cc_start: 0.8138 (m-80) cc_final: 0.7900 (m-10) REVERT: C 627 ASP cc_start: 0.7496 (t70) cc_final: 0.7287 (t0) REVERT: C 659 ILE cc_start: 0.9053 (pt) cc_final: 0.8730 (mm) REVERT: C 677 MET cc_start: 0.7749 (mtt) cc_final: 0.7541 (mtt) REVERT: D 119 LEU cc_start: 0.8543 (mm) cc_final: 0.8296 (mt) REVERT: D 129 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7375 (tm-30) REVERT: D 159 MET cc_start: 0.7684 (tpp) cc_final: 0.7352 (tpp) REVERT: D 249 PHE cc_start: 0.6366 (p90) cc_final: 0.4249 (m-80) REVERT: D 297 ASN cc_start: 0.8035 (m-40) cc_final: 0.7545 (m110) REVERT: D 335 THR cc_start: 0.9280 (p) cc_final: 0.8903 (t) REVERT: D 351 MET cc_start: 0.7993 (mmm) cc_final: 0.7605 (mmm) REVERT: D 353 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8094 (mmtp) REVERT: D 506 PHE cc_start: 0.7966 (t80) cc_final: 0.7731 (t80) REVERT: D 540 TYR cc_start: 0.6382 (t80) cc_final: 0.6042 (t80) REVERT: D 627 ASP cc_start: 0.7497 (t70) cc_final: 0.7296 (t0) REVERT: D 659 ILE cc_start: 0.9044 (pt) cc_final: 0.8719 (mm) REVERT: D 677 MET cc_start: 0.7874 (mtt) cc_final: 0.7625 (mtt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1342 time to fit residues: 120.5011 Evaluate side-chains 415 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 150 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 189 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 = 0.3636 r_free = 0.3636 target = 0.142346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.112316 restraints weight = 35523.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114818 restraints weight = 23935.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.115870 restraints weight = 18485.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116862 restraints weight = 16048.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117888 restraints weight = 14587.317| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21324 Z= 0.168 Angle : 0.753 11.487 28872 Z= 0.388 Chirality : 0.046 0.321 3308 Planarity : 0.005 0.069 3608 Dihedral : 6.044 37.838 2804 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.45 % Favored : 85.40 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.16), residues: 2568 helix: -0.06 (0.14), residues: 1492 sheet: -4.66 (0.50), residues: 40 loop : -4.02 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 733 TYR 0.023 0.002 TYR C 213 PHE 0.023 0.002 PHE C 249 TRP 0.014 0.001 TRP B 493 HIS 0.003 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00388 (21324) covalent geometry : angle 0.75311 (28872) hydrogen bonds : bond 0.03170 ( 764) hydrogen bonds : angle 4.20657 ( 2244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8629 (mm) cc_final: 0.8374 (mt) REVERT: A 159 MET cc_start: 0.7663 (tpp) cc_final: 0.6818 (tpp) REVERT: A 163 THR cc_start: 0.8686 (m) cc_final: 0.8403 (p) REVERT: A 249 PHE cc_start: 0.6399 (p90) cc_final: 0.4292 (m-80) REVERT: A 297 ASN cc_start: 0.8071 (m-40) cc_final: 0.7481 (m110) REVERT: A 335 THR cc_start: 0.9246 (p) cc_final: 0.8886 (t) REVERT: A 353 LYS cc_start: 0.9265 (mmtt) cc_final: 0.9049 (mmtm) REVERT: A 540 TYR cc_start: 0.6357 (t80) cc_final: 0.6133 (t80) REVERT: A 555 MET cc_start: 0.8702 (ttm) cc_final: 0.8398 (ttm) REVERT: A 659 ILE cc_start: 0.9029 (pt) cc_final: 0.8778 (mm) REVERT: B 159 MET cc_start: 0.7464 (tpp) cc_final: 0.6828 (tpp) REVERT: B 290 THR cc_start: 0.8633 (m) cc_final: 0.8327 (t) REVERT: B 297 ASN cc_start: 0.8317 (m110) cc_final: 0.7750 (m110) REVERT: B 320 MET cc_start: 0.8718 (mmm) cc_final: 0.8506 (mmm) REVERT: B 335 THR cc_start: 0.9231 (p) cc_final: 0.8722 (t) REVERT: B 555 MET cc_start: 0.8731 (ttm) cc_final: 0.8494 (ttm) REVERT: B 562 MET cc_start: 0.8796 (ttt) cc_final: 0.8564 (ttt) REVERT: B 569 PHE cc_start: 0.8105 (m-80) cc_final: 0.7860 (m-10) REVERT: B 679 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7611 (tp30) REVERT: C 119 LEU cc_start: 0.8616 (mm) cc_final: 0.8383 (mt) REVERT: C 159 MET cc_start: 0.7682 (tpp) cc_final: 0.7382 (tpp) REVERT: C 249 PHE cc_start: 0.6439 (p90) cc_final: 0.4310 (m-80) REVERT: C 297 ASN cc_start: 0.8076 (m-40) cc_final: 0.7598 (m-40) REVERT: C 335 THR cc_start: 0.9237 (p) cc_final: 0.8872 (t) REVERT: C 353 LYS cc_start: 0.9258 (mmtt) cc_final: 0.9026 (mmtm) REVERT: C 540 TYR cc_start: 0.6404 (t80) cc_final: 0.6163 (t80) REVERT: C 569 PHE cc_start: 0.8137 (m-80) cc_final: 0.7914 (m-10) REVERT: C 659 ILE cc_start: 0.9041 (pt) cc_final: 0.8814 (mm) REVERT: D 119 LEU cc_start: 0.8636 (mm) cc_final: 0.8375 (mt) REVERT: D 159 MET cc_start: 0.7656 (tpp) cc_final: 0.7334 (tpp) REVERT: D 249 PHE cc_start: 0.6401 (p90) cc_final: 0.4295 (m-80) REVERT: D 297 ASN cc_start: 0.8104 (m-40) cc_final: 0.7517 (m110) REVERT: D 335 THR cc_start: 0.9260 (p) cc_final: 0.8885 (t) REVERT: D 353 LYS cc_start: 0.9250 (mmtt) cc_final: 0.9026 (mmtm) REVERT: D 540 TYR cc_start: 0.6409 (t80) cc_final: 0.6179 (t80) REVERT: D 659 ILE cc_start: 0.9043 (pt) cc_final: 0.8794 (mm) REVERT: D 677 MET cc_start: 0.7797 (mtt) cc_final: 0.7588 (mtt) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.1278 time to fit residues: 112.3653 Evaluate side-chains 400 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 202 optimal weight: 2.9990 chunk 147 optimal weight: 0.0770 chunk 146 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 = 0.3681 r_free = 0.3681 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.116304 restraints weight = 34934.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118729 restraints weight = 23672.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119896 restraints weight = 18505.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121147 restraints weight = 15942.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121491 restraints weight = 14335.021| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21324 Z= 0.128 Angle : 0.743 12.290 28872 Z= 0.376 Chirality : 0.045 0.466 3308 Planarity : 0.004 0.063 3608 Dihedral : 5.887 37.609 2804 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.79 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.16), residues: 2568 helix: 0.29 (0.14), residues: 1432 sheet: -4.31 (0.39), residues: 60 loop : -4.01 (0.15), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 319 TYR 0.019 0.001 TYR D 213 PHE 0.018 0.001 PHE B 506 TRP 0.022 0.002 TRP D 481 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00280 (21324) covalent geometry : angle 0.74310 (28872) hydrogen bonds : bond 0.02957 ( 764) hydrogen bonds : angle 4.18722 ( 2244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8580 (mm) cc_final: 0.8351 (mt) REVERT: A 159 MET cc_start: 0.7657 (tpp) cc_final: 0.6820 (tpp) REVERT: A 249 PHE cc_start: 0.6238 (p90) cc_final: 0.4291 (m-80) REVERT: A 297 ASN cc_start: 0.7931 (m-40) cc_final: 0.7563 (m110) REVERT: A 335 THR cc_start: 0.9254 (p) cc_final: 0.8901 (t) REVERT: A 353 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8972 (mmtm) REVERT: A 506 PHE cc_start: 0.7896 (t80) cc_final: 0.7690 (t80) REVERT: A 540 TYR cc_start: 0.6304 (t80) cc_final: 0.6080 (t80) REVERT: A 555 MET cc_start: 0.8664 (ttm) cc_final: 0.8368 (ttm) REVERT: A 659 ILE cc_start: 0.8936 (pt) cc_final: 0.8735 (mm) REVERT: A 677 MET cc_start: 0.7620 (mtt) cc_final: 0.7362 (mtt) REVERT: B 119 LEU cc_start: 0.8627 (mm) cc_final: 0.8328 (mt) REVERT: B 159 MET cc_start: 0.7538 (tpp) cc_final: 0.6893 (tpp) REVERT: B 290 THR cc_start: 0.8568 (m) cc_final: 0.8223 (t) REVERT: B 297 ASN cc_start: 0.8235 (m110) cc_final: 0.7746 (m110) REVERT: B 335 THR cc_start: 0.9263 (p) cc_final: 0.8795 (t) REVERT: B 555 MET cc_start: 0.8647 (ttm) cc_final: 0.8408 (ttm) REVERT: B 562 MET cc_start: 0.8747 (ttt) cc_final: 0.8490 (ttt) REVERT: B 569 PHE cc_start: 0.8030 (m-80) cc_final: 0.7693 (m-10) REVERT: B 679 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7511 (tp30) REVERT: C 159 MET cc_start: 0.7691 (tpp) cc_final: 0.7375 (tpp) REVERT: C 249 PHE cc_start: 0.6246 (p90) cc_final: 0.4286 (m-80) REVERT: C 297 ASN cc_start: 0.7866 (m-40) cc_final: 0.7436 (m110) REVERT: C 335 THR cc_start: 0.9252 (p) cc_final: 0.8878 (t) REVERT: C 353 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8947 (mmtm) REVERT: C 506 PHE cc_start: 0.7894 (t80) cc_final: 0.7685 (t80) REVERT: C 540 TYR cc_start: 0.6297 (t80) cc_final: 0.6063 (t80) REVERT: C 569 PHE cc_start: 0.8067 (m-80) cc_final: 0.7825 (m-10) REVERT: C 677 MET cc_start: 0.7606 (mtt) cc_final: 0.7325 (mtt) REVERT: D 119 LEU cc_start: 0.8601 (mm) cc_final: 0.8376 (mt) REVERT: D 159 MET cc_start: 0.7652 (tpp) cc_final: 0.7330 (tpp) REVERT: D 249 PHE cc_start: 0.6204 (p90) cc_final: 0.4081 (m-80) REVERT: D 250 PHE cc_start: 0.7104 (p90) cc_final: 0.6897 (p90) REVERT: D 297 ASN cc_start: 0.7964 (m-40) cc_final: 0.7591 (m110) REVERT: D 335 THR cc_start: 0.9253 (p) cc_final: 0.8907 (t) REVERT: D 353 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8960 (mmtm) REVERT: D 506 PHE cc_start: 0.7899 (t80) cc_final: 0.7683 (t80) REVERT: D 540 TYR cc_start: 0.6369 (t80) cc_final: 0.6123 (t80) REVERT: D 659 ILE cc_start: 0.8998 (pt) cc_final: 0.8791 (mm) REVERT: D 677 MET cc_start: 0.7551 (mtt) cc_final: 0.7256 (mtt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.1286 time to fit residues: 114.3737 Evaluate side-chains 411 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 131 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 chunk 241 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117577 restraints weight = 34969.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119717 restraints weight = 24485.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120899 restraints weight = 19567.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.121803 restraints weight = 16827.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122260 restraints weight = 15344.532| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21324 Z= 0.128 Angle : 0.733 11.787 28872 Z= 0.370 Chirality : 0.045 0.508 3308 Planarity : 0.005 0.090 3608 Dihedral : 5.759 36.259 2804 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.67 % Favored : 86.18 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.16), residues: 2568 helix: 0.44 (0.14), residues: 1436 sheet: -4.06 (0.39), residues: 76 loop : -3.96 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 733 TYR 0.021 0.002 TYR C 213 PHE 0.019 0.001 PHE B 442 TRP 0.032 0.002 TRP B 481 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00279 (21324) covalent geometry : angle 0.73286 (28872) hydrogen bonds : bond 0.02802 ( 764) hydrogen bonds : angle 4.09785 ( 2244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 PHE cc_start: 0.6230 (p90) cc_final: 0.4048 (m-80) REVERT: A 280 LEU cc_start: 0.9212 (tp) cc_final: 0.8760 (tt) REVERT: A 297 ASN cc_start: 0.7912 (m-40) cc_final: 0.7617 (m110) REVERT: A 335 THR cc_start: 0.9269 (p) cc_final: 0.8929 (t) REVERT: A 353 LYS cc_start: 0.9236 (mmtt) cc_final: 0.8982 (mmtm) REVERT: A 506 PHE cc_start: 0.7995 (t80) cc_final: 0.7749 (t80) REVERT: A 540 TYR cc_start: 0.6383 (t80) cc_final: 0.6157 (t80) REVERT: A 555 MET cc_start: 0.8641 (ttm) cc_final: 0.8364 (ttm) REVERT: A 659 ILE cc_start: 0.8955 (pt) cc_final: 0.8752 (mm) REVERT: A 706 MET cc_start: 0.7769 (ttp) cc_final: 0.7090 (tmm) REVERT: B 119 LEU cc_start: 0.8592 (mm) cc_final: 0.8315 (mt) REVERT: B 159 MET cc_start: 0.7594 (tpp) cc_final: 0.6915 (tpp) REVERT: B 290 THR cc_start: 0.8496 (m) cc_final: 0.8060 (t) REVERT: B 297 ASN cc_start: 0.8237 (m110) cc_final: 0.7754 (m110) REVERT: B 335 THR cc_start: 0.9260 (p) cc_final: 0.8810 (t) REVERT: B 493 TRP cc_start: 0.8451 (t-100) cc_final: 0.8088 (t-100) REVERT: B 555 MET cc_start: 0.8628 (ttm) cc_final: 0.8378 (ttm) REVERT: B 562 MET cc_start: 0.8753 (ttt) cc_final: 0.8509 (ttt) REVERT: B 569 PHE cc_start: 0.8007 (m-80) cc_final: 0.7787 (m-10) REVERT: B 679 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7512 (tp30) REVERT: C 159 MET cc_start: 0.7800 (tpp) cc_final: 0.7497 (tpp) REVERT: C 249 PHE cc_start: 0.6225 (p90) cc_final: 0.4437 (m-80) REVERT: C 280 LEU cc_start: 0.9243 (tp) cc_final: 0.8792 (tt) REVERT: C 297 ASN cc_start: 0.7859 (m-40) cc_final: 0.7574 (m110) REVERT: C 335 THR cc_start: 0.9252 (p) cc_final: 0.8900 (t) REVERT: C 353 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8940 (mmtm) REVERT: C 506 PHE cc_start: 0.7984 (t80) cc_final: 0.7745 (t80) REVERT: C 540 TYR cc_start: 0.6361 (t80) cc_final: 0.6140 (t80) REVERT: C 569 PHE cc_start: 0.8132 (m-80) cc_final: 0.7892 (m-10) REVERT: C 578 MET cc_start: 0.8337 (tpp) cc_final: 0.8079 (tpp) REVERT: C 706 MET cc_start: 0.7785 (ttp) cc_final: 0.7124 (tmm) REVERT: D 159 MET cc_start: 0.7782 (tpp) cc_final: 0.7462 (tpp) REVERT: D 249 PHE cc_start: 0.6091 (p90) cc_final: 0.4022 (m-80) REVERT: D 250 PHE cc_start: 0.7275 (p90) cc_final: 0.7027 (p90) REVERT: D 280 LEU cc_start: 0.9213 (tp) cc_final: 0.8782 (tt) REVERT: D 297 ASN cc_start: 0.7887 (m-40) cc_final: 0.7630 (m110) REVERT: D 335 THR cc_start: 0.9292 (p) cc_final: 0.8950 (t) REVERT: D 353 LYS cc_start: 0.9220 (mmtt) cc_final: 0.8968 (mmtm) REVERT: D 506 PHE cc_start: 0.7987 (t80) cc_final: 0.7735 (t80) REVERT: D 540 TYR cc_start: 0.6439 (t80) cc_final: 0.6188 (t80) REVERT: D 572 MET cc_start: 0.8335 (tpp) cc_final: 0.8132 (tpp) REVERT: D 659 ILE cc_start: 0.8977 (pt) cc_final: 0.8775 (mm) REVERT: D 706 MET cc_start: 0.7757 (ttp) cc_final: 0.7089 (tmm) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1285 time to fit residues: 109.7720 Evaluate side-chains 412 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 164 optimal weight: 30.0000 chunk 172 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 = 0.3687 r_free = 0.3687 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116234 restraints weight = 35593.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118818 restraints weight = 23816.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120130 restraints weight = 18397.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120850 restraints weight = 15715.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121542 restraints weight = 14437.389| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21324 Z= 0.132 Angle : 0.739 11.514 28872 Z= 0.372 Chirality : 0.045 0.440 3308 Planarity : 0.005 0.092 3608 Dihedral : 5.678 34.746 2804 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.32 % Favored : 86.53 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.16), residues: 2568 helix: 0.51 (0.14), residues: 1420 sheet: -3.91 (0.40), residues: 76 loop : -3.91 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 733 TYR 0.023 0.002 TYR B 540 PHE 0.019 0.001 PHE B 506 TRP 0.017 0.001 TRP A 493 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00295 (21324) covalent geometry : angle 0.73855 (28872) hydrogen bonds : bond 0.02809 ( 764) hydrogen bonds : angle 4.13281 ( 2244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 531 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8201 (mmp) cc_final: 0.7658 (tpp) REVERT: A 249 PHE cc_start: 0.6141 (p90) cc_final: 0.4069 (m-80) REVERT: A 250 PHE cc_start: 0.7376 (p90) cc_final: 0.7116 (p90) REVERT: A 280 LEU cc_start: 0.9209 (tp) cc_final: 0.8741 (tt) REVERT: A 297 ASN cc_start: 0.7907 (m-40) cc_final: 0.7643 (m110) REVERT: A 335 THR cc_start: 0.9260 (p) cc_final: 0.8915 (t) REVERT: A 353 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8975 (mmtm) REVERT: A 506 PHE cc_start: 0.7864 (t80) cc_final: 0.7643 (t80) REVERT: A 555 MET cc_start: 0.8639 (ttm) cc_final: 0.8384 (ttm) REVERT: A 578 MET cc_start: 0.8528 (tpp) cc_final: 0.8269 (tpp) REVERT: A 659 ILE cc_start: 0.8958 (pt) cc_final: 0.8715 (mm) REVERT: A 706 MET cc_start: 0.7771 (ttp) cc_final: 0.7089 (tmm) REVERT: A 722 LYS cc_start: 0.6783 (tttt) cc_final: 0.6484 (ttpt) REVERT: B 119 LEU cc_start: 0.8586 (mm) cc_final: 0.8288 (mt) REVERT: B 159 MET cc_start: 0.7562 (tpp) cc_final: 0.7308 (tpp) REVERT: B 297 ASN cc_start: 0.8300 (m110) cc_final: 0.7834 (m110) REVERT: B 335 THR cc_start: 0.9260 (p) cc_final: 0.8800 (t) REVERT: B 493 TRP cc_start: 0.8510 (t-100) cc_final: 0.7989 (t-100) REVERT: B 555 MET cc_start: 0.8603 (ttm) cc_final: 0.8370 (ttm) REVERT: B 562 MET cc_start: 0.8710 (ttt) cc_final: 0.8470 (ttt) REVERT: B 569 PHE cc_start: 0.8143 (m-80) cc_final: 0.7811 (m-10) REVERT: B 679 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7491 (tp30) REVERT: B 722 LYS cc_start: 0.6470 (tttt) cc_final: 0.6188 (tttt) REVERT: C 159 MET cc_start: 0.7822 (tpp) cc_final: 0.6983 (tpp) REVERT: C 249 PHE cc_start: 0.6286 (p90) cc_final: 0.4438 (m-80) REVERT: C 280 LEU cc_start: 0.9244 (tp) cc_final: 0.8796 (tt) REVERT: C 297 ASN cc_start: 0.7861 (m-40) cc_final: 0.7591 (m110) REVERT: C 335 THR cc_start: 0.9251 (p) cc_final: 0.8893 (t) REVERT: C 353 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8944 (mmtm) REVERT: C 506 PHE cc_start: 0.7851 (t80) cc_final: 0.7635 (t80) REVERT: C 569 PHE cc_start: 0.8132 (m-80) cc_final: 0.7926 (m-10) REVERT: C 578 MET cc_start: 0.8482 (tpp) cc_final: 0.8154 (tpp) REVERT: C 706 MET cc_start: 0.7773 (ttp) cc_final: 0.7090 (tmm) REVERT: D 159 MET cc_start: 0.7784 (tpp) cc_final: 0.6930 (tpp) REVERT: D 163 THR cc_start: 0.8537 (m) cc_final: 0.8332 (p) REVERT: D 249 PHE cc_start: 0.6316 (p90) cc_final: 0.4088 (m-80) REVERT: D 250 PHE cc_start: 0.7342 (p90) cc_final: 0.7118 (p90) REVERT: D 280 LEU cc_start: 0.9220 (tp) cc_final: 0.8774 (tt) REVERT: D 297 ASN cc_start: 0.7883 (m-40) cc_final: 0.7628 (m110) REVERT: D 335 THR cc_start: 0.9271 (p) cc_final: 0.8917 (t) REVERT: D 353 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8975 (mmtm) REVERT: D 506 PHE cc_start: 0.7852 (t80) cc_final: 0.7623 (t80) REVERT: D 540 TYR cc_start: 0.6418 (t80) cc_final: 0.6210 (t80) REVERT: D 555 MET cc_start: 0.8535 (ttm) cc_final: 0.8301 (ttm) REVERT: D 569 PHE cc_start: 0.8308 (m-80) cc_final: 0.8086 (m-10) REVERT: D 578 MET cc_start: 0.8463 (tpp) cc_final: 0.8148 (tpp) REVERT: D 659 ILE cc_start: 0.8977 (pt) cc_final: 0.8730 (mm) REVERT: D 706 MET cc_start: 0.7761 (ttp) cc_final: 0.7056 (tmm) outliers start: 1 outliers final: 0 residues processed: 532 average time/residue: 0.1260 time to fit residues: 110.2213 Evaluate side-chains 404 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 234 optimal weight: 0.0470 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 155 optimal weight: 0.0870 chunk 99 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 176 optimal weight: 0.0070 chunk 157 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 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 = 0.3714 r_free = 0.3714 target = 0.148864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118869 restraints weight = 35472.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121354 restraints weight = 23821.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122713 restraints weight = 18580.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123850 restraints weight = 15874.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124000 restraints weight = 14262.542| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21324 Z= 0.124 Angle : 0.711 11.613 28872 Z= 0.361 Chirality : 0.043 0.349 3308 Planarity : 0.005 0.090 3608 Dihedral : 5.568 33.678 2804 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.36 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2568 helix: 0.54 (0.14), residues: 1440 sheet: -3.84 (0.42), residues: 76 loop : -3.88 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 733 TYR 0.038 0.002 TYR A 540 PHE 0.020 0.001 PHE B 506 TRP 0.023 0.002 TRP D 481 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00262 (21324) covalent geometry : angle 0.71099 (28872) hydrogen bonds : bond 0.02700 ( 764) hydrogen bonds : angle 4.04909 ( 2244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.43 seconds wall clock time: 64 minutes 8.44 seconds (3848.44 seconds total)