Starting phenix.real_space_refine on Wed Jun 18 01:20:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvn_20494/06_2025/6pvn_20494.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvn_20494/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pvn_20494/06_2025/6pvn_20494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvn_20494/06_2025/6pvn_20494.map" model { file = "/net/cci-nas-00/data/ceres_data/6pvn_20494/06_2025/6pvn_20494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvn_20494/06_2025/6pvn_20494.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.27, per 1000 atoms: 0.73 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: 5.92 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 1.96 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: 7.48 Time building geometry restraints manager: 7.02 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: 0.11 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 81.210 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: 0.040 Extract box with map and model: 1.770 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 55.820 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP C 692 HIS 0.012 0.002 HIS B 301 PHE 0.043 0.003 PHE D 542 TYR 0.036 0.002 TYR D 213 ARG 0.011 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.33380 ( 764) hydrogen bonds : angle 10.39934 ( 2244) covalent geometry : bond 0.00613 (21324) covalent geometry : angle 1.32808 (28872) *********************** 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 : 2.383 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: 0.7556 (tpp) REVERT: A 335 THR cc_start: 0.9343 (p) cc_final: 0.9079 (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: 0.8012 (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: 0.5802 (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: 0.7369 (mm) REVERT: A 748 PHE cc_start: 0.7359 (p90) cc_final: 0.6787 (p90) REVERT: B 159 MET cc_start: 0.7754 (tpp) cc_final: 0.6872 (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: 0.6041 (ttmt) REVERT: B 734 ILE cc_start: 0.7914 (mt) cc_final: 0.7588 (mm) REVERT: B 748 PHE cc_start: 0.7556 (p90) cc_final: 0.7050 (p90) REVERT: C 159 MET cc_start: 0.7880 (tpp) cc_final: 0.7564 (tpp) REVERT: C 335 THR cc_start: 0.9344 (p) cc_final: 0.9115 (t) REVERT: C 353 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8508 (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: 0.5827 (t80) REVERT: C 584 LEU cc_start: 0.8317 (tm) cc_final: 0.8020 (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: 0.7356 (pp20) REVERT: C 734 ILE cc_start: 0.7683 (mt) cc_final: 0.7351 (mm) REVERT: C 748 PHE cc_start: 0.7428 (p90) cc_final: 0.7009 (p90) REVERT: D 159 MET cc_start: 0.7876 (tpp) cc_final: 0.7541 (tpp) REVERT: D 335 THR cc_start: 0.9339 (p) cc_final: 0.9109 (t) REVERT: D 353 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8499 (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: 0.8004 (ttpp) REVERT: D 479 MET cc_start: 0.0774 (mmm) cc_final: 0.0303 (mtm) REVERT: D 540 TYR cc_start: 0.6091 (t80) cc_final: 0.5836 (t80) REVERT: D 584 LEU cc_start: 0.8311 (tm) cc_final: 0.8015 (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: 0.7309 (mm) REVERT: D 748 PHE cc_start: 0.7396 (p90) cc_final: 0.6947 (p90) outliers start: 28 outliers final: 8 residues processed: 868 average time/residue: 0.3815 time to fit residues: 520.2409 Evaluate side-chains 487 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 479 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 570 GLN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 426 HIS B 483 GLN B 570 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 570 GLN D 585 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.111059 restraints weight = 35514.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.113278 restraints weight = 24388.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.114553 restraints weight = 19209.942| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21324 Z= 0.213 Angle : 0.870 13.404 28872 Z= 0.457 Chirality : 0.047 0.243 3308 Planarity : 0.007 0.081 3608 Dihedral : 7.764 44.662 2804 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.47 % Allowed : 14.49 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.13), residues: 2568 helix: -2.41 (0.11), residues: 1436 sheet: None (None), residues: 0 loop : -4.25 (0.14), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 739 HIS 0.004 0.001 HIS B 160 PHE 0.032 0.002 PHE D 249 TYR 0.023 0.002 TYR D 213 ARG 0.008 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.05491 ( 764) hydrogen bonds : angle 5.16991 ( 2244) covalent geometry : bond 0.00473 (21324) covalent geometry : angle 0.86967 (28872) *********************** 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 659 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 2.357 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: symmetry clash REVERT: A 121 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8482 (mtpt) REVERT: A 129 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 159 MET cc_start: 0.7832 (tpp) cc_final: 0.6721 (tpp) REVERT: A 163 THR cc_start: 0.8679 (m) cc_final: 0.8387 (p) REVERT: A 207 GLU cc_start: 0.8045 (pt0) cc_final: 0.7826 (pm20) REVERT: A 297 ASN cc_start: 0.7775 (m-40) cc_final: 0.7060 (m-40) REVERT: A 335 THR cc_start: 0.9286 (p) cc_final: 0.8931 (t) REVERT: A 353 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8540 (mmtm) REVERT: A 498 SER cc_start: 0.9019 (t) cc_final: 0.8691 (p) REVERT: A 540 TYR cc_start: 0.6530 (t80) cc_final: 0.6162 (t80) REVERT: A 555 MET cc_start: 0.8710 (ttm) cc_final: 0.8447 (ttm) REVERT: A 627 ASP cc_start: 0.7624 (t70) cc_final: 0.7378 (t0) REVERT: A 659 ILE cc_start: 0.9033 (pt) cc_final: 0.8774 (mm) REVERT: A 677 MET cc_start: 0.7810 (mtt) cc_final: 0.7574 (mtt) REVERT: A 734 ILE cc_start: 0.7411 (mt) cc_final: 0.6387 (tt) REVERT: B 129 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7618 (tm-30) REVERT: B 159 MET cc_start: 0.7750 (tpp) cc_final: 0.6634 (tpp) REVERT: B 248 VAL cc_start: 0.8277 (m) cc_final: 0.8053 (p) REVERT: B 282 MET cc_start: 0.8224 (mmm) cc_final: 0.7868 (mmt) REVERT: B 297 ASN cc_start: 0.7969 (m-40) cc_final: 0.7433 (m110) REVERT: B 335 THR cc_start: 0.9289 (p) cc_final: 0.8848 (t) REVERT: B 464 ARG cc_start: 0.6145 (tpm170) cc_final: 0.5832 (mmt-90) REVERT: B 479 MET cc_start: 0.0762 (mmm) cc_final: 0.0478 (mtm) REVERT: B 497 ILE cc_start: 0.9206 (tp) cc_final: 0.8699 (tt) REVERT: B 534 ILE cc_start: 0.9268 (tp) cc_final: 0.9056 (tp) REVERT: B 569 PHE cc_start: 0.8086 (m-10) cc_final: 0.7824 (m-10) REVERT: B 605 LEU cc_start: 0.8998 (mp) cc_final: 0.8516 (mt) REVERT: B 677 MET cc_start: 0.7744 (mtt) cc_final: 0.7420 (mtt) REVERT: B 679 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7651 (tp30) REVERT: B 685 SER cc_start: 0.9198 (t) cc_final: 0.8974 (t) REVERT: C 129 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 159 MET cc_start: 0.7850 (tpp) cc_final: 0.6723 (tpp) REVERT: C 163 THR cc_start: 0.8650 (m) cc_final: 0.8344 (p) REVERT: C 207 GLU cc_start: 0.8063 (pt0) cc_final: 0.7826 (pm20) REVERT: C 260 TYR cc_start: 0.8877 (t80) cc_final: 0.8677 (t80) REVERT: C 297 ASN cc_start: 0.7797 (m-40) cc_final: 0.7057 (m-40) REVERT: C 335 THR cc_start: 0.9275 (p) cc_final: 0.8912 (t) REVERT: C 353 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8531 (mmtm) REVERT: C 445 PHE cc_start: 0.9108 (t80) cc_final: 0.8791 (t80) REVERT: C 498 SER cc_start: 0.9027 (t) cc_final: 0.8696 (p) REVERT: C 513 LEU cc_start: 0.8045 (mt) cc_final: 0.7796 (mt) REVERT: C 540 TYR cc_start: 0.6550 (t80) cc_final: 0.6177 (t80) REVERT: C 555 MET cc_start: 0.8681 (ttm) cc_final: 0.8457 (ttm) REVERT: C 605 LEU cc_start: 0.9139 (mp) cc_final: 0.8582 (mt) REVERT: C 627 ASP cc_start: 0.7602 (t70) cc_final: 0.7341 (t0) REVERT: C 659 ILE cc_start: 0.9031 (pt) cc_final: 0.8784 (mm) REVERT: C 734 ILE cc_start: 0.7426 (mt) cc_final: 0.6409 (tt) REVERT: C 748 PHE cc_start: 0.7832 (p90) cc_final: 0.7436 (p90) REVERT: D 129 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 159 MET cc_start: 0.7839 (tpp) cc_final: 0.6714 (tpp) REVERT: D 163 THR cc_start: 0.8680 (m) cc_final: 0.8381 (p) REVERT: D 207 GLU cc_start: 0.8040 (pt0) cc_final: 0.7819 (pm20) REVERT: D 260 TYR cc_start: 0.8882 (t80) cc_final: 0.8674 (t80) REVERT: D 297 ASN cc_start: 0.7773 (m-40) cc_final: 0.7074 (m-40) REVERT: D 335 THR cc_start: 0.9280 (p) cc_final: 0.8914 (t) REVERT: D 353 LYS cc_start: 0.9187 (mmtt) cc_final: 0.8536 (mmtm) REVERT: D 498 SER cc_start: 0.9024 (t) cc_final: 0.8694 (p) REVERT: D 513 LEU cc_start: 0.8010 (mt) cc_final: 0.7799 (mt) REVERT: D 540 TYR cc_start: 0.6548 (t80) cc_final: 0.6172 (t80) REVERT: D 555 MET cc_start: 0.8678 (ttm) cc_final: 0.8461 (ttm) REVERT: D 605 LEU cc_start: 0.9132 (mp) cc_final: 0.8593 (mt) REVERT: D 627 ASP cc_start: 0.7639 (t70) cc_final: 0.7373 (t0) REVERT: D 659 ILE cc_start: 0.9042 (pt) cc_final: 0.8791 (mm) REVERT: D 677 MET cc_start: 0.7859 (mtt) cc_final: 0.7649 (mtt) REVERT: D 734 ILE cc_start: 0.7535 (mt) cc_final: 0.6560 (tt) REVERT: D 748 PHE cc_start: 0.7828 (p90) cc_final: 0.7433 (p90) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.3997 time to fit residues: 416.9295 Evaluate side-chains 469 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 155 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 198 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 523 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 HIS D 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113364 restraints weight = 35115.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115894 restraints weight = 23317.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117158 restraints weight = 17917.097| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4115 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= 0.152 Angle : 0.777 12.043 28872 Z= 0.403 Chirality : 0.045 0.269 3308 Planarity : 0.005 0.072 3608 Dihedral : 7.060 37.889 2804 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.38 % Favored : 84.42 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.14), residues: 2568 helix: -1.55 (0.12), residues: 1484 sheet: -5.99 (0.28), residues: 20 loop : -4.35 (0.14), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 739 HIS 0.004 0.001 HIS D 523 PHE 0.026 0.002 PHE A 250 TYR 0.021 0.002 TYR D 208 ARG 0.007 0.000 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 764) hydrogen bonds : angle 4.53206 ( 2244) covalent geometry : bond 0.00326 (21324) covalent geometry : angle 0.77719 (28872) *********************** 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 603 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 2.582 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: 0.8443 (mm) cc_final: 0.8148 (mt) REVERT: A 121 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8480 (mtpt) REVERT: A 159 MET cc_start: 0.7763 (tpp) cc_final: 0.7529 (tpp) REVERT: A 207 GLU cc_start: 0.8029 (pt0) cc_final: 0.7771 (pm20) REVERT: A 297 ASN cc_start: 0.7959 (m-40) cc_final: 0.7224 (m110) REVERT: A 327 ARG cc_start: 0.7263 (tpt170) cc_final: 0.6976 (tpt90) REVERT: A 335 THR cc_start: 0.9269 (p) cc_final: 0.8911 (t) REVERT: A 353 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8432 (mmtm) REVERT: A 540 TYR cc_start: 0.6490 (t80) cc_final: 0.6149 (t80) REVERT: A 555 MET cc_start: 0.8628 (ttm) cc_final: 0.8350 (ttm) REVERT: A 605 LEU cc_start: 0.9282 (mt) cc_final: 0.9053 (mm) REVERT: A 677 MET cc_start: 0.7916 (mtt) cc_final: 0.7577 (mtt) REVERT: A 687 GLU cc_start: 0.7146 (tp30) cc_final: 0.6573 (pp20) REVERT: A 734 ILE cc_start: 0.7238 (mt) cc_final: 0.6839 (mm) REVERT: B 159 MET cc_start: 0.7443 (tpp) cc_final: 0.6896 (tpp) REVERT: B 248 VAL cc_start: 0.8284 (m) cc_final: 0.8083 (p) REVERT: B 297 ASN cc_start: 0.7953 (m-40) cc_final: 0.7374 (m110) REVERT: B 327 ARG cc_start: 0.7155 (tpt170) cc_final: 0.6932 (tpt170) REVERT: B 335 THR cc_start: 0.9285 (p) cc_final: 0.8805 (t) REVERT: B 351 MET cc_start: 0.8437 (mmm) cc_final: 0.8219 (mmm) REVERT: B 523 HIS cc_start: 0.7976 (m-70) cc_final: 0.7501 (m-70) REVERT: B 605 LEU cc_start: 0.9033 (mp) cc_final: 0.8571 (mt) REVERT: B 677 MET cc_start: 0.7619 (mtt) cc_final: 0.7296 (mtt) REVERT: C 119 LEU cc_start: 0.8414 (mm) cc_final: 0.8129 (mt) REVERT: C 121 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8462 (mtpt) REVERT: C 159 MET cc_start: 0.7787 (tpp) cc_final: 0.7547 (tpp) REVERT: C 207 GLU cc_start: 0.8017 (pt0) cc_final: 0.7776 (pm20) REVERT: C 248 VAL cc_start: 0.7933 (p) cc_final: 0.7597 (p) REVERT: C 297 ASN cc_start: 0.7900 (m-40) cc_final: 0.7362 (m110) REVERT: C 327 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6961 (tpt90) REVERT: C 335 THR cc_start: 0.9280 (p) cc_final: 0.8924 (t) REVERT: C 353 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8415 (mmtm) REVERT: C 540 TYR cc_start: 0.6503 (t80) cc_final: 0.6145 (t80) REVERT: C 555 MET cc_start: 0.8650 (ttm) cc_final: 0.8394 (ttm) REVERT: C 605 LEU cc_start: 0.9111 (mp) cc_final: 0.8607 (mt) REVERT: C 687 GLU cc_start: 0.7181 (tp30) cc_final: 0.6551 (pp20) REVERT: C 734 ILE cc_start: 0.7260 (mt) cc_final: 0.6842 (mm) REVERT: D 119 LEU cc_start: 0.8442 (mm) cc_final: 0.8147 (mt) REVERT: D 121 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8445 (mtpt) REVERT: D 159 MET cc_start: 0.7769 (tpp) cc_final: 0.7530 (tpp) REVERT: D 207 GLU cc_start: 0.8022 (pt0) cc_final: 0.7762 (pm20) REVERT: D 248 VAL cc_start: 0.7939 (p) cc_final: 0.7619 (p) REVERT: D 297 ASN cc_start: 0.7897 (m-40) cc_final: 0.7372 (m110) REVERT: D 327 ARG cc_start: 0.7271 (tpt170) cc_final: 0.6974 (tpt90) REVERT: D 335 THR cc_start: 0.9283 (p) cc_final: 0.8939 (t) REVERT: D 353 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8414 (mmtm) REVERT: D 540 TYR cc_start: 0.6499 (t80) cc_final: 0.6151 (t80) REVERT: D 555 MET cc_start: 0.8629 (ttm) cc_final: 0.8387 (ttm) REVERT: D 605 LEU cc_start: 0.9118 (mp) cc_final: 0.8612 (mt) REVERT: D 677 MET cc_start: 0.7876 (mtt) cc_final: 0.7581 (mtt) REVERT: D 687 GLU cc_start: 0.7139 (tp30) cc_final: 0.6548 (pp20) REVERT: D 722 LYS cc_start: 0.6786 (tttt) cc_final: 0.6182 (tttt) REVERT: D 734 ILE cc_start: 0.7241 (mt) cc_final: 0.6856 (mm) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 0.3595 time to fit residues: 353.3992 Evaluate side-chains 439 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 162 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 244 HIS A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS C 585 HIS D 197 ASN D 244 HIS D 256 HIS D 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.139715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.109587 restraints weight = 35964.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111961 restraints weight = 23998.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113302 restraints weight = 18597.429| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 21324 Z= 0.198 Angle : 0.800 10.652 28872 Z= 0.414 Chirality : 0.047 0.327 3308 Planarity : 0.005 0.084 3608 Dihedral : 6.811 37.483 2804 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.68 % Favored : 85.12 % Rotamer: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.15), residues: 2568 helix: -1.07 (0.13), residues: 1472 sheet: -5.94 (0.28), residues: 20 loop : -4.24 (0.15), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 481 HIS 0.004 0.001 HIS A 417 PHE 0.031 0.002 PHE C 249 TYR 0.020 0.002 TYR B 213 ARG 0.003 0.000 ARG B 733 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 764) hydrogen bonds : angle 4.52098 ( 2244) covalent geometry : bond 0.00451 (21324) covalent geometry : angle 0.80048 (28872) *********************** 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 585 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 584 time to evaluate : 4.827 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 159 MET cc_start: 0.7710 (tpp) cc_final: 0.7450 (tpp) REVERT: A 297 ASN cc_start: 0.8136 (m-40) cc_final: 0.7434 (m110) REVERT: A 335 THR cc_start: 0.9292 (p) cc_final: 0.8920 (t) REVERT: A 540 TYR cc_start: 0.6553 (t80) cc_final: 0.6152 (t80) REVERT: A 555 MET cc_start: 0.8669 (ttm) cc_final: 0.8442 (ttm) REVERT: A 569 PHE cc_start: 0.8386 (m-80) cc_final: 0.8138 (m-10) REVERT: A 605 LEU cc_start: 0.9280 (mt) cc_final: 0.9069 (mm) REVERT: A 677 MET cc_start: 0.7933 (mtt) cc_final: 0.7704 (mtt) REVERT: A 687 GLU cc_start: 0.7160 (tp30) cc_final: 0.6428 (pp20) REVERT: B 129 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 159 MET cc_start: 0.7423 (tpp) cc_final: 0.6913 (tpp) REVERT: B 297 ASN cc_start: 0.8023 (m-40) cc_final: 0.7614 (m110) REVERT: B 320 MET cc_start: 0.8717 (mmm) cc_final: 0.8371 (mmm) REVERT: B 335 THR cc_start: 0.9277 (p) cc_final: 0.8812 (t) REVERT: B 605 LEU cc_start: 0.9070 (mp) cc_final: 0.8640 (mt) REVERT: B 677 MET cc_start: 0.7720 (mtt) cc_final: 0.7476 (mtt) REVERT: C 129 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 159 MET cc_start: 0.7780 (tpp) cc_final: 0.7508 (tpp) REVERT: C 248 VAL cc_start: 0.8114 (p) cc_final: 0.7886 (p) REVERT: C 297 ASN cc_start: 0.8155 (m-40) cc_final: 0.7445 (m110) REVERT: C 335 THR cc_start: 0.9288 (p) cc_final: 0.8926 (t) REVERT: C 540 TYR cc_start: 0.6529 (t80) cc_final: 0.6134 (t80) REVERT: C 555 MET cc_start: 0.8618 (ttm) cc_final: 0.8357 (ttm) REVERT: C 569 PHE cc_start: 0.8392 (m-80) cc_final: 0.8188 (m-10) REVERT: C 605 LEU cc_start: 0.9161 (mp) cc_final: 0.8678 (mt) REVERT: C 627 ASP cc_start: 0.7535 (t70) cc_final: 0.7334 (t0) REVERT: C 677 MET cc_start: 0.7772 (mtt) cc_final: 0.7546 (mtt) REVERT: C 687 GLU cc_start: 0.7118 (tp30) cc_final: 0.6448 (pp20) REVERT: D 129 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 159 MET cc_start: 0.7754 (tpp) cc_final: 0.7499 (tpp) REVERT: D 248 VAL cc_start: 0.8101 (p) cc_final: 0.7897 (p) REVERT: D 297 ASN cc_start: 0.8175 (m-40) cc_final: 0.7467 (m110) REVERT: D 335 THR cc_start: 0.9347 (p) cc_final: 0.8971 (t) REVERT: D 540 TYR cc_start: 0.6515 (t80) cc_final: 0.6128 (t80) REVERT: D 569 PHE cc_start: 0.8420 (m-80) cc_final: 0.8146 (m-10) REVERT: D 605 LEU cc_start: 0.9113 (mp) cc_final: 0.8655 (mt) REVERT: D 627 ASP cc_start: 0.7571 (t70) cc_final: 0.7358 (t0) REVERT: D 677 MET cc_start: 0.7981 (mtt) cc_final: 0.7681 (mtt) REVERT: D 687 GLU cc_start: 0.7107 (tp30) cc_final: 0.6431 (pp20) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.3726 time to fit residues: 357.3658 Evaluate side-chains 426 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 253 optimal weight: 0.0050 chunk 134 optimal weight: 1.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 585 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 585 HIS D 585 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112600 restraints weight = 35596.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.115010 restraints weight = 23612.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116349 restraints weight = 18283.169| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21324 Z= 0.141 Angle : 0.745 12.348 28872 Z= 0.386 Chirality : 0.044 0.222 3308 Planarity : 0.005 0.077 3608 Dihedral : 6.494 38.369 2804 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.91 % Favored : 84.74 % Rotamer: Outliers : 0.22 % Allowed : 3.97 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.15), residues: 2568 helix: -0.73 (0.13), residues: 1492 sheet: -5.81 (0.30), residues: 20 loop : -4.15 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 739 HIS 0.003 0.001 HIS C 417 PHE 0.021 0.002 PHE C 249 TYR 0.043 0.002 TYR C 650 ARG 0.004 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 764) hydrogen bonds : angle 4.33128 ( 2244) covalent geometry : bond 0.00312 (21324) covalent geometry : angle 0.74533 (28872) *********************** 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 559 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 554 time to evaluate : 3.469 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: A 119 LEU cc_start: 0.8409 (mm) cc_final: 0.8170 (mt) REVERT: A 159 MET cc_start: 0.7656 (tpp) cc_final: 0.7355 (tpp) REVERT: A 177 LEU cc_start: 0.9121 (mt) cc_final: 0.8819 (mp) REVERT: A 297 ASN cc_start: 0.7984 (m-40) cc_final: 0.7443 (m110) REVERT: A 335 THR cc_start: 0.9299 (p) cc_final: 0.8907 (t) REVERT: A 540 TYR cc_start: 0.6492 (t80) cc_final: 0.6164 (t80) REVERT: A 555 MET cc_start: 0.8661 (ttm) cc_final: 0.8427 (ttm) REVERT: A 605 LEU cc_start: 0.9291 (mt) cc_final: 0.9059 (mm) REVERT: A 677 MET cc_start: 0.7821 (mtt) cc_final: 0.7507 (mtt) REVERT: A 687 GLU cc_start: 0.6870 (tp30) cc_final: 0.6489 (pp20) REVERT: A 722 LYS cc_start: 0.6941 (tttt) cc_final: 0.6729 (tttt) REVERT: B 159 MET cc_start: 0.7430 (tpp) cc_final: 0.6860 (tpp) REVERT: B 297 ASN cc_start: 0.7808 (m-40) cc_final: 0.7553 (m110) REVERT: B 327 ARG cc_start: 0.6520 (tpt170) cc_final: 0.6289 (tpt-90) REVERT: B 335 THR cc_start: 0.9259 (p) cc_final: 0.8774 (t) REVERT: B 677 MET cc_start: 0.7536 (mtt) cc_final: 0.7277 (mtt) REVERT: B 679 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7420 (tp30) REVERT: B 722 LYS cc_start: 0.6790 (tttt) cc_final: 0.6577 (tttt) REVERT: C 119 LEU cc_start: 0.8377 (mm) cc_final: 0.8166 (mt) REVERT: C 159 MET cc_start: 0.7672 (tpp) cc_final: 0.7383 (tpp) REVERT: C 297 ASN cc_start: 0.8067 (m-40) cc_final: 0.7487 (m110) REVERT: C 335 THR cc_start: 0.9290 (p) cc_final: 0.8901 (t) REVERT: C 540 TYR cc_start: 0.6513 (t80) cc_final: 0.6163 (t80) REVERT: C 605 LEU cc_start: 0.9133 (mp) cc_final: 0.8652 (mt) REVERT: C 687 GLU cc_start: 0.6904 (tp30) cc_final: 0.6489 (pp20) REVERT: D 119 LEU cc_start: 0.8419 (mm) cc_final: 0.8192 (mt) REVERT: D 159 MET cc_start: 0.7679 (tpp) cc_final: 0.7417 (tpp) REVERT: D 177 LEU cc_start: 0.9122 (mt) cc_final: 0.8825 (mp) REVERT: D 297 ASN cc_start: 0.8084 (m-40) cc_final: 0.7538 (m110) REVERT: D 335 THR cc_start: 0.9302 (p) cc_final: 0.8894 (t) REVERT: D 540 TYR cc_start: 0.6454 (t80) cc_final: 0.6120 (t80) REVERT: D 605 LEU cc_start: 0.9149 (mp) cc_final: 0.8659 (mt) REVERT: D 677 MET cc_start: 0.7709 (mtt) cc_final: 0.7443 (mtt) REVERT: D 687 GLU cc_start: 0.6893 (tp30) cc_final: 0.6479 (pp20) outliers start: 5 outliers final: 4 residues processed: 559 average time/residue: 0.4457 time to fit residues: 410.9356 Evaluate side-chains 404 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 400 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 14 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 chunk 252 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 191 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** B 735 ASN D 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115386 restraints weight = 35025.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117895 restraints weight = 23187.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119200 restraints weight = 17880.278| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5088 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= 0.130 Angle : 0.732 11.621 28872 Z= 0.373 Chirality : 0.045 0.394 3308 Planarity : 0.004 0.067 3608 Dihedral : 6.145 39.463 2804 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.14 % Favored : 85.71 % 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 : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2568 helix: -0.43 (0.13), residues: 1492 sheet: -4.20 (0.40), residues: 52 loop : -4.07 (0.16), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 481 HIS 0.004 0.001 HIS D 301 PHE 0.017 0.001 PHE D 250 TYR 0.024 0.001 TYR A 213 ARG 0.003 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 764) hydrogen bonds : angle 4.19699 ( 2244) covalent geometry : bond 0.00276 (21324) covalent geometry : angle 0.73235 (28872) *********************** 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 571 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8597 (mm) cc_final: 0.8347 (mt) REVERT: A 159 MET cc_start: 0.7621 (tpp) cc_final: 0.7387 (tpp) REVERT: A 290 THR cc_start: 0.8630 (m) cc_final: 0.8142 (t) REVERT: A 297 ASN cc_start: 0.8010 (m-40) cc_final: 0.7648 (m110) REVERT: A 335 THR cc_start: 0.9315 (p) cc_final: 0.8899 (t) REVERT: A 488 MET cc_start: 0.7279 (mtt) cc_final: 0.6794 (mtm) REVERT: A 540 TYR cc_start: 0.6471 (t80) cc_final: 0.6120 (t80) REVERT: A 555 MET cc_start: 0.8685 (ttm) cc_final: 0.8394 (ttm) REVERT: A 677 MET cc_start: 0.7735 (mtt) cc_final: 0.7441 (mtt) REVERT: A 687 GLU cc_start: 0.6669 (tp30) cc_final: 0.6355 (pp20) REVERT: A 722 LYS cc_start: 0.6933 (tttt) cc_final: 0.6367 (tppt) REVERT: B 119 LEU cc_start: 0.8620 (mm) cc_final: 0.8357 (mt) REVERT: B 129 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 159 MET cc_start: 0.7465 (tpp) cc_final: 0.6895 (tpp) REVERT: B 335 THR cc_start: 0.9263 (p) cc_final: 0.8809 (t) REVERT: B 562 MET cc_start: 0.8886 (ttt) cc_final: 0.8640 (ttt) REVERT: B 677 MET cc_start: 0.7498 (mtt) cc_final: 0.7213 (mtt) REVERT: B 679 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7439 (tp30) REVERT: B 722 LYS cc_start: 0.6833 (tttt) cc_final: 0.6137 (tttt) REVERT: C 119 LEU cc_start: 0.8574 (mm) cc_final: 0.8333 (mt) REVERT: C 159 MET cc_start: 0.7654 (tpp) cc_final: 0.7376 (tpp) REVERT: C 249 PHE cc_start: 0.6166 (p90) cc_final: 0.4074 (m-80) REVERT: C 297 ASN cc_start: 0.8039 (m-40) cc_final: 0.7660 (m110) REVERT: C 335 THR cc_start: 0.9325 (p) cc_final: 0.8928 (t) REVERT: C 488 MET cc_start: 0.7270 (mtt) cc_final: 0.6794 (mtm) REVERT: C 540 TYR cc_start: 0.6474 (t80) cc_final: 0.6130 (t80) REVERT: C 687 GLU cc_start: 0.6755 (tp30) cc_final: 0.6332 (pp20) REVERT: C 722 LYS cc_start: 0.6947 (tttt) cc_final: 0.6692 (tppt) REVERT: D 119 LEU cc_start: 0.8600 (mm) cc_final: 0.8339 (mt) REVERT: D 159 MET cc_start: 0.7687 (tpp) cc_final: 0.7435 (tpp) REVERT: D 249 PHE cc_start: 0.6223 (p90) cc_final: 0.4095 (m-80) REVERT: D 297 ASN cc_start: 0.8027 (m-40) cc_final: 0.7643 (m110) REVERT: D 335 THR cc_start: 0.9297 (p) cc_final: 0.8932 (t) REVERT: D 488 MET cc_start: 0.7283 (mtt) cc_final: 0.6808 (mtm) REVERT: D 540 TYR cc_start: 0.6457 (t80) cc_final: 0.6104 (t80) REVERT: D 677 MET cc_start: 0.7641 (mtt) cc_final: 0.7362 (mtt) REVERT: D 687 GLU cc_start: 0.6754 (tp30) cc_final: 0.6330 (pp20) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.4055 time to fit residues: 378.6650 Evaluate side-chains 407 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 4.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 107 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 735 ASN C 735 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111870 restraints weight = 35444.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114377 restraints weight = 23807.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115613 restraints weight = 18359.379| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21324 Z= 0.173 Angle : 0.781 12.504 28872 Z= 0.396 Chirality : 0.046 0.306 3308 Planarity : 0.005 0.067 3608 Dihedral : 6.093 37.748 2804 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.64 % Favored : 85.20 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2568 helix: -0.16 (0.13), residues: 1476 sheet: -5.43 (0.37), residues: 20 loop : -4.04 (0.15), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 481 HIS 0.005 0.001 HIS D 585 PHE 0.027 0.002 PHE B 249 TYR 0.024 0.002 TYR B 213 ARG 0.006 0.000 ARG B 733 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 764) hydrogen bonds : angle 4.28567 ( 2244) covalent geometry : bond 0.00401 (21324) covalent geometry : angle 0.78146 (28872) *********************** 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 532 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 6.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8613 (mm) cc_final: 0.8300 (mt) REVERT: A 159 MET cc_start: 0.7660 (tpp) cc_final: 0.7420 (tpp) REVERT: A 297 ASN cc_start: 0.8085 (m-40) cc_final: 0.7477 (m110) REVERT: A 335 THR cc_start: 0.9312 (p) cc_final: 0.8915 (t) REVERT: A 540 TYR cc_start: 0.6579 (t80) cc_final: 0.6270 (t80) REVERT: A 555 MET cc_start: 0.8691 (ttm) cc_final: 0.8486 (ttm) REVERT: A 569 PHE cc_start: 0.8398 (m-80) cc_final: 0.8140 (m-10) REVERT: A 677 MET cc_start: 0.7855 (mtt) cc_final: 0.7630 (mtt) REVERT: A 687 GLU cc_start: 0.6795 (tp30) cc_final: 0.6359 (pp20) REVERT: B 119 LEU cc_start: 0.8640 (mm) cc_final: 0.8333 (mt) REVERT: B 129 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 159 MET cc_start: 0.7486 (tpp) cc_final: 0.6904 (tpp) REVERT: B 297 ASN cc_start: 0.8208 (m110) cc_final: 0.7660 (m110) REVERT: B 335 THR cc_start: 0.9311 (p) cc_final: 0.8815 (t) REVERT: B 351 MET cc_start: 0.8325 (mmm) cc_final: 0.8092 (mmm) REVERT: B 479 MET cc_start: -0.1191 (mmm) cc_final: -0.1644 (mmm) REVERT: B 562 MET cc_start: 0.8857 (ttt) cc_final: 0.8597 (ttt) REVERT: B 679 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7552 (tp30) REVERT: B 722 LYS cc_start: 0.6606 (tttt) cc_final: 0.6296 (tttt) REVERT: C 119 LEU cc_start: 0.8571 (mm) cc_final: 0.8281 (mt) REVERT: C 159 MET cc_start: 0.7697 (tpp) cc_final: 0.7496 (tpp) REVERT: C 297 ASN cc_start: 0.8206 (m-40) cc_final: 0.7664 (m110) REVERT: C 335 THR cc_start: 0.9314 (p) cc_final: 0.8919 (t) REVERT: C 531 VAL cc_start: 0.9662 (m) cc_final: 0.9321 (p) REVERT: C 540 TYR cc_start: 0.6454 (t80) cc_final: 0.6134 (t80) REVERT: C 569 PHE cc_start: 0.8180 (m-80) cc_final: 0.7948 (m-10) REVERT: C 687 GLU cc_start: 0.6786 (tp30) cc_final: 0.6344 (pp20) REVERT: D 119 LEU cc_start: 0.8619 (mm) cc_final: 0.8299 (mt) REVERT: D 159 MET cc_start: 0.7714 (tpp) cc_final: 0.7482 (tpp) REVERT: D 297 ASN cc_start: 0.8160 (m-40) cc_final: 0.7591 (m110) REVERT: D 335 THR cc_start: 0.9315 (p) cc_final: 0.8911 (t) REVERT: D 540 TYR cc_start: 0.6505 (t80) cc_final: 0.6196 (t80) REVERT: D 569 PHE cc_start: 0.8189 (m-80) cc_final: 0.7962 (m-10) REVERT: D 677 MET cc_start: 0.7888 (mtt) cc_final: 0.7654 (mtt) REVERT: D 687 GLU cc_start: 0.6792 (tp30) cc_final: 0.6325 (pp20) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4033 time to fit residues: 351.8655 Evaluate side-chains 407 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 95 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 252 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 243 optimal weight: 0.9990 chunk 234 optimal weight: 0.0870 chunk 149 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 231 optimal weight: 0.2980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 251 ASN ** B 297 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 = 0.3672 r_free = 0.3672 target = 0.145403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115735 restraints weight = 35578.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118294 restraints weight = 23784.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119467 restraints weight = 18417.207| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21324 Z= 0.132 Angle : 0.755 12.449 28872 Z= 0.380 Chirality : 0.046 0.469 3308 Planarity : 0.004 0.063 3608 Dihedral : 5.940 37.876 2804 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.29 % Favored : 85.55 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.16), residues: 2568 helix: 0.02 (0.14), residues: 1484 sheet: -4.57 (0.46), residues: 40 loop : -4.15 (0.15), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 739 HIS 0.004 0.001 HIS D 301 PHE 0.019 0.001 PHE A 506 TYR 0.021 0.001 TYR D 213 ARG 0.013 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 764) hydrogen bonds : angle 4.16609 ( 2244) covalent geometry : bond 0.00284 (21324) covalent geometry : angle 0.75537 (28872) *********************** 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 : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8613 (mm) cc_final: 0.8329 (mt) REVERT: A 159 MET cc_start: 0.7666 (tpp) cc_final: 0.7441 (tpp) REVERT: A 297 ASN cc_start: 0.8024 (m-40) cc_final: 0.7673 (m110) REVERT: A 335 THR cc_start: 0.9286 (p) cc_final: 0.8894 (t) REVERT: A 540 TYR cc_start: 0.6420 (t80) cc_final: 0.6131 (t80) REVERT: A 555 MET cc_start: 0.8710 (ttm) cc_final: 0.8455 (ttm) REVERT: A 677 MET cc_start: 0.7699 (mtt) cc_final: 0.7346 (mtt) REVERT: A 687 GLU cc_start: 0.6572 (tp30) cc_final: 0.6327 (pp20) REVERT: A 722 LYS cc_start: 0.6888 (tttt) cc_final: 0.6620 (ttpt) REVERT: B 119 LEU cc_start: 0.8598 (mm) cc_final: 0.8314 (mt) REVERT: B 129 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 159 MET cc_start: 0.7444 (tpp) cc_final: 0.6811 (tpp) REVERT: B 290 THR cc_start: 0.8560 (m) cc_final: 0.8267 (t) REVERT: B 297 ASN cc_start: 0.8117 (m110) cc_final: 0.7605 (m110) REVERT: B 335 THR cc_start: 0.9308 (p) cc_final: 0.8818 (t) REVERT: B 351 MET cc_start: 0.8334 (mmm) cc_final: 0.8091 (mmm) REVERT: B 371 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8161 (ttp-170) REVERT: B 479 MET cc_start: -0.1448 (mmm) cc_final: -0.1845 (mmm) REVERT: B 562 MET cc_start: 0.8894 (ttt) cc_final: 0.8675 (ttt) REVERT: B 565 TYR cc_start: 0.7651 (m-10) cc_final: 0.7331 (m-80) REVERT: B 572 MET cc_start: 0.8276 (tpp) cc_final: 0.8045 (tpp) REVERT: C 119 LEU cc_start: 0.8580 (mm) cc_final: 0.8302 (mt) REVERT: C 159 MET cc_start: 0.7686 (tpp) cc_final: 0.7427 (tpp) REVERT: C 297 ASN cc_start: 0.8022 (m-40) cc_final: 0.7688 (m110) REVERT: C 335 THR cc_start: 0.9284 (p) cc_final: 0.8916 (t) REVERT: C 540 TYR cc_start: 0.6371 (t80) cc_final: 0.6077 (t80) REVERT: C 569 PHE cc_start: 0.8196 (m-80) cc_final: 0.7939 (m-10) REVERT: C 687 GLU cc_start: 0.6514 (tp30) cc_final: 0.6257 (pp20) REVERT: D 119 LEU cc_start: 0.8608 (mm) cc_final: 0.8322 (mt) REVERT: D 159 MET cc_start: 0.7671 (tpp) cc_final: 0.7445 (tpp) REVERT: D 249 PHE cc_start: 0.6296 (p90) cc_final: 0.4178 (m-80) REVERT: D 297 ASN cc_start: 0.8073 (m-40) cc_final: 0.7722 (m110) REVERT: D 335 THR cc_start: 0.9290 (p) cc_final: 0.8903 (t) REVERT: D 540 TYR cc_start: 0.6279 (t80) cc_final: 0.5992 (t80) REVERT: D 572 MET cc_start: 0.8382 (tpp) cc_final: 0.8083 (tpp) REVERT: D 677 MET cc_start: 0.7770 (mtt) cc_final: 0.7420 (mtt) REVERT: D 687 GLU cc_start: 0.6512 (tp30) cc_final: 0.6204 (pp20) REVERT: D 722 LYS cc_start: 0.6727 (tttt) cc_final: 0.6463 (tttt) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.3084 time to fit residues: 274.4916 Evaluate side-chains 405 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 190 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 452 ASN B 645 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.141458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111513 restraints weight = 35684.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.113909 restraints weight = 24097.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115053 restraints weight = 18756.077| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21324 Z= 0.172 Angle : 0.775 11.961 28872 Z= 0.395 Chirality : 0.048 0.449 3308 Planarity : 0.004 0.062 3608 Dihedral : 5.897 36.148 2804 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.98 % Favored : 85.86 % Rotamer: Outliers : 0.04 % Allowed : 0.93 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2568 helix: 0.15 (0.14), residues: 1464 sheet: -5.25 (0.39), residues: 20 loop : -3.98 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 481 HIS 0.003 0.001 HIS D 745 PHE 0.024 0.002 PHE C 249 TYR 0.025 0.002 TYR B 540 ARG 0.008 0.000 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 764) hydrogen bonds : angle 4.29150 ( 2244) covalent geometry : bond 0.00397 (21324) covalent geometry : angle 0.77540 (28872) *********************** 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 520 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8663 (mm) cc_final: 0.8366 (mt) REVERT: A 159 MET cc_start: 0.7679 (tpp) cc_final: 0.7445 (tpp) REVERT: A 297 ASN cc_start: 0.8130 (m-40) cc_final: 0.7607 (m110) REVERT: A 335 THR cc_start: 0.9308 (p) cc_final: 0.8917 (t) REVERT: A 531 VAL cc_start: 0.9688 (m) cc_final: 0.9343 (p) REVERT: A 540 TYR cc_start: 0.6489 (t80) cc_final: 0.6254 (t80) REVERT: A 555 MET cc_start: 0.8689 (ttm) cc_final: 0.8449 (ttm) REVERT: A 578 MET cc_start: 0.8456 (tpp) cc_final: 0.8198 (tpp) REVERT: A 687 GLU cc_start: 0.6707 (tp30) cc_final: 0.6311 (pp20) REVERT: B 119 LEU cc_start: 0.8633 (mm) cc_final: 0.8359 (mt) REVERT: B 129 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 138 LEU cc_start: 0.8720 (mp) cc_final: 0.8487 (mp) REVERT: B 159 MET cc_start: 0.7493 (tpp) cc_final: 0.6897 (tpp) REVERT: B 290 THR cc_start: 0.8618 (m) cc_final: 0.8345 (t) REVERT: B 297 ASN cc_start: 0.8226 (m110) cc_final: 0.7638 (m110) REVERT: B 335 THR cc_start: 0.9340 (p) cc_final: 0.8878 (t) REVERT: B 371 ARG cc_start: 0.8551 (ttp-170) cc_final: 0.8314 (ttp-170) REVERT: B 479 MET cc_start: -0.1203 (mmm) cc_final: -0.1649 (mmm) REVERT: B 562 MET cc_start: 0.8931 (ttt) cc_final: 0.8715 (ttt) REVERT: B 565 TYR cc_start: 0.7823 (m-10) cc_final: 0.7601 (m-80) REVERT: B 679 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7642 (tp30) REVERT: B 685 SER cc_start: 0.9365 (t) cc_final: 0.9100 (t) REVERT: B 733 ARG cc_start: 0.7034 (mmm160) cc_final: 0.6783 (mmm160) REVERT: C 119 LEU cc_start: 0.8650 (mm) cc_final: 0.8347 (mt) REVERT: C 297 ASN cc_start: 0.8177 (m-40) cc_final: 0.7658 (m110) REVERT: C 335 THR cc_start: 0.9314 (p) cc_final: 0.8921 (t) REVERT: C 440 MET cc_start: 0.8487 (mtp) cc_final: 0.8269 (mtp) REVERT: C 531 VAL cc_start: 0.9688 (m) cc_final: 0.9355 (p) REVERT: C 540 TYR cc_start: 0.6461 (t80) cc_final: 0.6220 (t80) REVERT: C 679 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7551 (tp30) REVERT: C 687 GLU cc_start: 0.6712 (tp30) cc_final: 0.6259 (pp20) REVERT: C 722 LYS cc_start: 0.7110 (tttt) cc_final: 0.6714 (tppt) REVERT: D 119 LEU cc_start: 0.8724 (mm) cc_final: 0.8394 (mt) REVERT: D 159 MET cc_start: 0.7733 (tpp) cc_final: 0.7492 (tpp) REVERT: D 297 ASN cc_start: 0.8216 (m-40) cc_final: 0.7697 (m110) REVERT: D 335 THR cc_start: 0.9276 (p) cc_final: 0.8883 (t) REVERT: D 531 VAL cc_start: 0.9681 (m) cc_final: 0.9338 (p) REVERT: D 540 TYR cc_start: 0.6488 (t80) cc_final: 0.6236 (t80) REVERT: D 677 MET cc_start: 0.7873 (mtt) cc_final: 0.7555 (mtt) REVERT: D 679 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7640 (tp30) REVERT: D 687 GLU cc_start: 0.6702 (tp30) cc_final: 0.6244 (pp20) outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.2739 time to fit residues: 231.7567 Evaluate side-chains 401 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 645 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109781 restraints weight = 35780.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112124 restraints weight = 24223.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113199 restraints weight = 18983.130| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21324 Z= 0.186 Angle : 0.812 12.183 28872 Z= 0.410 Chirality : 0.048 0.419 3308 Planarity : 0.004 0.061 3608 Dihedral : 5.977 34.866 2804 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.90 % Favored : 85.94 % Rotamer: Outliers : 0.04 % Allowed : 0.62 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2568 helix: 0.16 (0.14), residues: 1452 sheet: -5.10 (0.40), residues: 20 loop : -3.99 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 481 HIS 0.006 0.001 HIS C 585 PHE 0.027 0.002 PHE B 249 TYR 0.023 0.002 TYR D 213 ARG 0.006 0.000 ARG D 733 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 764) hydrogen bonds : angle 4.46112 ( 2244) covalent geometry : bond 0.00434 (21324) covalent geometry : angle 0.81182 (28872) ********************** 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 482 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8693 (mm) cc_final: 0.8343 (mt) REVERT: A 159 MET cc_start: 0.7679 (tpp) cc_final: 0.7464 (tpp) REVERT: A 297 ASN cc_start: 0.8196 (m-40) cc_final: 0.7654 (m110) REVERT: A 335 THR cc_start: 0.9330 (p) cc_final: 0.8918 (t) REVERT: A 345 LEU cc_start: 0.9354 (tp) cc_final: 0.9134 (tt) REVERT: A 479 MET cc_start: -0.0839 (mmm) cc_final: -0.1339 (mmm) REVERT: A 531 VAL cc_start: 0.9707 (m) cc_final: 0.9374 (p) REVERT: A 555 MET cc_start: 0.8714 (ttm) cc_final: 0.8490 (ttm) REVERT: A 578 MET cc_start: 0.8638 (tpp) cc_final: 0.8408 (tpp) REVERT: A 679 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7647 (tp30) REVERT: A 687 GLU cc_start: 0.6740 (tp30) cc_final: 0.6285 (pp20) REVERT: A 722 LYS cc_start: 0.6983 (tttt) cc_final: 0.6630 (tppt) REVERT: B 129 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7727 (tm-30) REVERT: B 159 MET cc_start: 0.7594 (tpp) cc_final: 0.6999 (tpp) REVERT: B 263 GLU cc_start: 0.8556 (pm20) cc_final: 0.8353 (mp0) REVERT: B 290 THR cc_start: 0.8651 (m) cc_final: 0.8418 (t) REVERT: B 297 ASN cc_start: 0.8290 (m110) cc_final: 0.7585 (m110) REVERT: B 335 THR cc_start: 0.9338 (p) cc_final: 0.8865 (t) REVERT: B 479 MET cc_start: -0.1174 (mmm) cc_final: -0.1490 (mmm) REVERT: B 531 VAL cc_start: 0.9695 (m) cc_final: 0.9318 (p) REVERT: B 565 TYR cc_start: 0.7917 (m-10) cc_final: 0.7685 (m-80) REVERT: B 679 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7690 (tp30) REVERT: B 728 PHE cc_start: 0.7025 (t80) cc_final: 0.6674 (p90) REVERT: C 119 LEU cc_start: 0.8667 (mm) cc_final: 0.8299 (mt) REVERT: C 297 ASN cc_start: 0.8212 (m-40) cc_final: 0.7625 (m110) REVERT: C 335 THR cc_start: 0.9340 (p) cc_final: 0.8952 (t) REVERT: C 345 LEU cc_start: 0.9361 (tp) cc_final: 0.9149 (tt) REVERT: C 440 MET cc_start: 0.8427 (mtp) cc_final: 0.8192 (mtp) REVERT: C 479 MET cc_start: -0.0799 (mmm) cc_final: -0.1258 (mmm) REVERT: C 531 VAL cc_start: 0.9700 (m) cc_final: 0.9398 (p) REVERT: C 687 GLU cc_start: 0.6764 (tp30) cc_final: 0.6217 (pp20) REVERT: C 722 LYS cc_start: 0.7078 (tttt) cc_final: 0.6637 (tppt) REVERT: D 119 LEU cc_start: 0.8671 (mm) cc_final: 0.8353 (mt) REVERT: D 139 LEU cc_start: 0.9059 (mm) cc_final: 0.8856 (tp) REVERT: D 159 MET cc_start: 0.7829 (tpp) cc_final: 0.7626 (tpp) REVERT: D 297 ASN cc_start: 0.8244 (m-40) cc_final: 0.7637 (m110) REVERT: D 335 THR cc_start: 0.9291 (p) cc_final: 0.8891 (t) REVERT: D 345 LEU cc_start: 0.9373 (tp) cc_final: 0.9111 (tt) REVERT: D 479 MET cc_start: -0.0775 (mmm) cc_final: -0.1209 (mmm) REVERT: D 531 VAL cc_start: 0.9703 (m) cc_final: 0.9355 (p) REVERT: D 687 GLU cc_start: 0.6772 (tp30) cc_final: 0.6255 (pp20) REVERT: D 722 LYS cc_start: 0.6583 (tttt) cc_final: 0.6247 (tttt) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.3784 time to fit residues: 303.2541 Evaluate side-chains 379 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 193 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111946 restraints weight = 35755.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114381 restraints weight = 23744.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115590 restraints weight = 18392.283| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5832 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= 0.143 Angle : 0.772 12.089 28872 Z= 0.390 Chirality : 0.046 0.391 3308 Planarity : 0.005 0.062 3608 Dihedral : 5.902 35.390 2804 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.82 % Favored : 86.02 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.16), residues: 2568 helix: 0.27 (0.14), residues: 1440 sheet: -4.42 (0.46), residues: 40 loop : -3.93 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 481 HIS 0.011 0.001 HIS B 426 PHE 0.020 0.001 PHE B 506 TYR 0.037 0.002 TYR A 540 ARG 0.018 0.000 ARG B 733 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 764) hydrogen bonds : angle 4.36826 ( 2244) covalent geometry : bond 0.00323 (21324) covalent geometry : angle 0.77250 (28872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9373.85 seconds wall clock time: 174 minutes 35.42 seconds (10475.42 seconds total)