Starting phenix.real_space_refine on Sat Sep 28 22:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_20494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_20494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_20494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_20494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvn_20494/09_2024/6pvn_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.89, per 1000 atoms: 0.52 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: 5.20 Conformation dependent library (CDL) restraints added in 2.7 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: 1.85 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: 5.37 Time building geometry restraints manager: 6.20 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 115 through 758) selection = (chain 'B' and resid 115 through 758) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 43.750 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- 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= 0.398 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 *********************** 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 fitting. rotamer outliers: 28 poor density : 848 time to evaluate : 2.840 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: 0.3040 time to fit residues: 406.4104 Evaluate side-chains 487 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 479 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3506 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= 0.304 Angle : 0.869 13.394 28872 Z= 0.457 Chirality : 0.047 0.240 3308 Planarity : 0.007 0.081 3608 Dihedral : 7.760 44.660 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: -2.40 (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 *********************** 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 660 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 2.300 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: 0.8976 (mmmt) cc_final: 0.8486 (mtpt) REVERT: A 129 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 159 MET cc_start: 0.7836 (tpp) cc_final: 0.6722 (tpp) REVERT: A 163 THR cc_start: 0.8653 (m) cc_final: 0.8360 (p) REVERT: A 207 GLU cc_start: 0.8030 (pt0) cc_final: 0.7821 (pm20) REVERT: A 297 ASN cc_start: 0.7748 (m-40) cc_final: 0.7035 (m-40) REVERT: A 335 THR cc_start: 0.9266 (p) cc_final: 0.8919 (t) REVERT: A 353 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8547 (mmtm) REVERT: A 498 SER cc_start: 0.9041 (t) cc_final: 0.8684 (p) REVERT: A 540 TYR cc_start: 0.6563 (t80) cc_final: 0.6196 (t80) REVERT: A 555 MET cc_start: 0.8707 (ttm) cc_final: 0.8439 (ttm) REVERT: A 627 ASP cc_start: 0.7607 (t70) cc_final: 0.7378 (t0) REVERT: A 659 ILE cc_start: 0.9046 (pt) cc_final: 0.8789 (mm) REVERT: A 677 MET cc_start: 0.7794 (mtt) cc_final: 0.7563 (mtt) REVERT: A 734 ILE cc_start: 0.7429 (mt) cc_final: 0.6375 (tt) REVERT: B 129 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 159 MET cc_start: 0.7765 (tpp) cc_final: 0.6641 (tpp) REVERT: B 248 VAL cc_start: 0.8298 (m) cc_final: 0.8072 (p) REVERT: B 282 MET cc_start: 0.8272 (mmm) cc_final: 0.7902 (mmt) REVERT: B 297 ASN cc_start: 0.7963 (m-40) cc_final: 0.7420 (m110) REVERT: B 335 THR cc_start: 0.9294 (p) cc_final: 0.8875 (t) REVERT: B 464 ARG cc_start: 0.6130 (tpm170) cc_final: 0.5818 (mmt-90) REVERT: B 479 MET cc_start: 0.0742 (mmm) cc_final: 0.0465 (mtm) REVERT: B 497 ILE cc_start: 0.9168 (tp) cc_final: 0.8659 (tt) REVERT: B 534 ILE cc_start: 0.9276 (tp) cc_final: 0.9056 (tp) REVERT: B 569 PHE cc_start: 0.8084 (m-10) cc_final: 0.7823 (m-10) REVERT: B 605 LEU cc_start: 0.8992 (mp) cc_final: 0.8508 (mt) REVERT: B 677 MET cc_start: 0.7730 (mtt) cc_final: 0.7411 (mtt) REVERT: B 679 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7645 (tp30) REVERT: B 685 SER cc_start: 0.9209 (t) cc_final: 0.8981 (t) REVERT: C 129 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 159 MET cc_start: 0.7860 (tpp) cc_final: 0.6729 (tpp) REVERT: C 163 THR cc_start: 0.8650 (m) cc_final: 0.8348 (p) REVERT: C 207 GLU cc_start: 0.8046 (pt0) cc_final: 0.7824 (pm20) REVERT: C 297 ASN cc_start: 0.7777 (m-40) cc_final: 0.7036 (m-40) REVERT: C 335 THR cc_start: 0.9267 (p) cc_final: 0.8918 (t) REVERT: C 353 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8540 (mmtm) REVERT: C 445 PHE cc_start: 0.9105 (t80) cc_final: 0.8784 (t80) REVERT: C 498 SER cc_start: 0.9043 (t) cc_final: 0.8688 (p) REVERT: C 513 LEU cc_start: 0.8036 (mt) cc_final: 0.7789 (mt) REVERT: C 540 TYR cc_start: 0.6582 (t80) cc_final: 0.6203 (t80) REVERT: C 555 MET cc_start: 0.8696 (ttm) cc_final: 0.8467 (ttm) REVERT: C 605 LEU cc_start: 0.9142 (mp) cc_final: 0.8589 (mt) REVERT: C 627 ASP cc_start: 0.7585 (t70) cc_final: 0.7337 (t0) REVERT: C 659 ILE cc_start: 0.9052 (pt) cc_final: 0.8808 (mm) REVERT: C 734 ILE cc_start: 0.7416 (mt) cc_final: 0.6382 (tt) REVERT: C 748 PHE cc_start: 0.7813 (p90) cc_final: 0.7422 (p90) REVERT: D 129 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 159 MET cc_start: 0.7839 (tpp) cc_final: 0.6712 (tpp) REVERT: D 163 THR cc_start: 0.8656 (m) cc_final: 0.8365 (p) REVERT: D 207 GLU cc_start: 0.8038 (pt0) cc_final: 0.7808 (pm20) REVERT: D 260 TYR cc_start: 0.8876 (t80) cc_final: 0.8664 (t80) REVERT: D 297 ASN cc_start: 0.7763 (m-40) cc_final: 0.7056 (m-40) REVERT: D 335 THR cc_start: 0.9267 (p) cc_final: 0.8911 (t) REVERT: D 353 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8537 (mmtm) REVERT: D 498 SER cc_start: 0.9041 (t) cc_final: 0.8686 (p) REVERT: D 513 LEU cc_start: 0.7981 (mt) cc_final: 0.7773 (mt) REVERT: D 540 TYR cc_start: 0.6594 (t80) cc_final: 0.6216 (t80) REVERT: D 555 MET cc_start: 0.8678 (ttm) cc_final: 0.8453 (ttm) REVERT: D 605 LEU cc_start: 0.9127 (mp) cc_final: 0.8590 (mt) REVERT: D 627 ASP cc_start: 0.7601 (t70) cc_final: 0.7348 (t0) REVERT: D 659 ILE cc_start: 0.9054 (pt) cc_final: 0.8802 (mm) REVERT: D 734 ILE cc_start: 0.7543 (mt) cc_final: 0.6552 (tt) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.2925 time to fit residues: 301.6601 Evaluate side-chains 468 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 0.0470 chunk 193 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 0.0050 chunk 251 optimal weight: 0.2980 chunk 207 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 186 optimal weight: 0.1980 overall best weight: 0.3092 ------------------------------------------------------------------------------- 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 D 523 HIS D 585 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21324 Z= 0.174 Angle : 0.767 11.425 28872 Z= 0.396 Chirality : 0.044 0.256 3308 Planarity : 0.005 0.071 3608 Dihedral : 6.876 38.985 2804 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 15.03 % Favored : 84.74 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -3.96 (0.14), residues: 2568 helix: -1.48 (0.12), residues: 1468 sheet: -4.87 (0.37), residues: 40 loop : -4.29 (0.14), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 493 HIS 0.004 0.001 HIS A 417 PHE 0.021 0.002 PHE B 542 TYR 0.022 0.002 TYR D 208 ARG 0.007 0.000 ARG B 464 *********************** 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 645 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 2.670 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: 0.8493 (mm) cc_final: 0.8224 (mt) REVERT: A 121 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8473 (mtpt) REVERT: A 159 MET cc_start: 0.7671 (tpp) cc_final: 0.7403 (tpp) REVERT: A 216 GLN cc_start: 0.8793 (tt0) cc_final: 0.8409 (mt0) REVERT: A 248 VAL cc_start: 0.7959 (p) cc_final: 0.7738 (p) REVERT: A 249 PHE cc_start: 0.6370 (p90) cc_final: 0.4226 (m-80) REVERT: A 297 ASN cc_start: 0.7862 (m-40) cc_final: 0.7255 (m110) REVERT: A 335 THR cc_start: 0.9322 (p) cc_final: 0.8986 (t) REVERT: A 353 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8429 (mmtm) REVERT: A 540 TYR cc_start: 0.6439 (t80) cc_final: 0.6133 (t80) REVERT: A 555 MET cc_start: 0.8612 (ttm) cc_final: 0.8278 (ttm) REVERT: A 605 LEU cc_start: 0.9249 (mt) cc_final: 0.9046 (mm) REVERT: A 637 ILE cc_start: 0.8264 (mp) cc_final: 0.7972 (pt) REVERT: A 677 MET cc_start: 0.7760 (mtt) cc_final: 0.7363 (mtt) REVERT: A 687 GLU cc_start: 0.6877 (tp30) cc_final: 0.6586 (pp20) REVERT: A 722 LYS cc_start: 0.6801 (tttt) cc_final: 0.6522 (tttt) REVERT: A 734 ILE cc_start: 0.7017 (mt) cc_final: 0.5872 (tt) REVERT: B 121 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8452 (mtpt) REVERT: B 159 MET cc_start: 0.7435 (tpp) cc_final: 0.6725 (tpp) REVERT: B 260 TYR cc_start: 0.8731 (t80) cc_final: 0.7803 (t80) REVERT: B 297 ASN cc_start: 0.7774 (m-40) cc_final: 0.7439 (m110) REVERT: B 327 ARG cc_start: 0.6968 (tpt170) cc_final: 0.6751 (tpt170) REVERT: B 335 THR cc_start: 0.9281 (p) cc_final: 0.8809 (t) REVERT: B 351 MET cc_start: 0.8425 (mmm) cc_final: 0.8208 (mmm) REVERT: B 523 HIS cc_start: 0.7854 (m-70) cc_final: 0.7624 (m90) REVERT: B 555 MET cc_start: 0.8818 (ttp) cc_final: 0.8548 (ttm) REVERT: B 569 PHE cc_start: 0.8078 (m-10) cc_final: 0.7866 (m-10) REVERT: B 605 LEU cc_start: 0.8956 (mp) cc_final: 0.8482 (mt) REVERT: B 677 MET cc_start: 0.7452 (mtt) cc_final: 0.7182 (mtt) REVERT: C 119 LEU cc_start: 0.8464 (mm) cc_final: 0.8188 (mt) REVERT: C 121 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8494 (mtpt) REVERT: C 159 MET cc_start: 0.7692 (tpp) cc_final: 0.7413 (tpp) REVERT: C 216 GLN cc_start: 0.8781 (tt0) cc_final: 0.8413 (mt0) REVERT: C 248 VAL cc_start: 0.7979 (p) cc_final: 0.7763 (p) REVERT: C 249 PHE cc_start: 0.6389 (p90) cc_final: 0.4225 (m-80) REVERT: C 297 ASN cc_start: 0.7895 (m-40) cc_final: 0.7267 (m110) REVERT: C 335 THR cc_start: 0.9308 (p) cc_final: 0.8970 (t) REVERT: C 353 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8380 (mmtm) REVERT: C 540 TYR cc_start: 0.6471 (t80) cc_final: 0.6143 (t80) REVERT: C 555 MET cc_start: 0.8623 (ttm) cc_final: 0.8328 (ttm) REVERT: C 605 LEU cc_start: 0.9064 (mp) cc_final: 0.8587 (mt) REVERT: C 637 ILE cc_start: 0.8279 (mp) cc_final: 0.7990 (pt) REVERT: C 687 GLU cc_start: 0.6951 (tp30) cc_final: 0.6640 (pp20) REVERT: C 722 LYS cc_start: 0.6555 (tttt) cc_final: 0.6161 (tttt) REVERT: C 734 ILE cc_start: 0.7023 (mt) cc_final: 0.5881 (tt) REVERT: C 748 PHE cc_start: 0.7637 (p90) cc_final: 0.7375 (p90) REVERT: D 119 LEU cc_start: 0.8489 (mm) cc_final: 0.8213 (mt) REVERT: D 121 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8469 (mtpt) REVERT: D 159 MET cc_start: 0.7669 (tpp) cc_final: 0.7398 (tpp) REVERT: D 216 GLN cc_start: 0.8803 (tt0) cc_final: 0.8422 (mt0) REVERT: D 248 VAL cc_start: 0.7916 (p) cc_final: 0.7697 (p) REVERT: D 249 PHE cc_start: 0.6314 (p90) cc_final: 0.4207 (m-80) REVERT: D 335 THR cc_start: 0.9324 (p) cc_final: 0.8985 (t) REVERT: D 353 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8398 (mmtm) REVERT: D 540 TYR cc_start: 0.6490 (t80) cc_final: 0.6172 (t80) REVERT: D 555 MET cc_start: 0.8597 (ttm) cc_final: 0.8325 (ttm) REVERT: D 605 LEU cc_start: 0.9062 (mp) cc_final: 0.8554 (mt) REVERT: D 637 ILE cc_start: 0.8318 (mp) cc_final: 0.8036 (pt) REVERT: D 687 GLU cc_start: 0.6925 (tp30) cc_final: 0.6601 (pp20) REVERT: D 722 LYS cc_start: 0.6794 (tttt) cc_final: 0.6540 (tttt) REVERT: D 734 ILE cc_start: 0.7080 (mt) cc_final: 0.5850 (tt) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.2773 time to fit residues: 284.7197 Evaluate side-chains 463 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 221 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 256 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 256 HIS C 585 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21324 Z= 0.196 Angle : 0.751 11.799 28872 Z= 0.386 Chirality : 0.044 0.310 3308 Planarity : 0.005 0.082 3608 Dihedral : 6.506 38.957 2804 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.06 % Favored : 85.79 % Rotamer: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % 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: -3.37 (0.15), residues: 2568 helix: -0.91 (0.13), residues: 1456 sheet: -4.54 (0.38), residues: 56 loop : -4.12 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 493 HIS 0.003 0.001 HIS C 417 PHE 0.021 0.001 PHE D 250 TYR 0.018 0.001 TYR B 208 ARG 0.004 0.000 ARG B 464 *********************** 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 607 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 606 time to evaluate : 2.538 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: 0.8577 (mm) cc_final: 0.8308 (mt) REVERT: A 121 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8463 (mtpt) REVERT: A 159 MET cc_start: 0.7642 (tpp) cc_final: 0.7364 (tpp) REVERT: A 249 PHE cc_start: 0.6236 (p90) cc_final: 0.4158 (m-80) REVERT: A 268 LEU cc_start: 0.8965 (pp) cc_final: 0.8748 (pp) REVERT: A 297 ASN cc_start: 0.7967 (m-40) cc_final: 0.7448 (m110) REVERT: A 335 THR cc_start: 0.9326 (p) cc_final: 0.8962 (t) REVERT: A 353 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8327 (mmtp) REVERT: A 540 TYR cc_start: 0.6551 (t80) cc_final: 0.6206 (t80) REVERT: A 555 MET cc_start: 0.8564 (ttm) cc_final: 0.8325 (ttm) REVERT: A 562 MET cc_start: 0.8699 (ttt) cc_final: 0.8434 (ttt) REVERT: A 569 PHE cc_start: 0.8339 (m-80) cc_final: 0.8073 (m-10) REVERT: A 677 MET cc_start: 0.7773 (mtt) cc_final: 0.7460 (mtt) REVERT: A 687 GLU cc_start: 0.6928 (tp30) cc_final: 0.6548 (pp20) REVERT: B 121 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8383 (mtpt) REVERT: B 129 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7578 (tm-30) REVERT: B 159 MET cc_start: 0.7427 (tpp) cc_final: 0.6893 (tpp) REVERT: B 260 TYR cc_start: 0.8681 (t80) cc_final: 0.8469 (t80) REVERT: B 320 MET cc_start: 0.8596 (mmm) cc_final: 0.8246 (mmm) REVERT: B 335 THR cc_start: 0.9246 (p) cc_final: 0.8777 (t) REVERT: B 410 ASN cc_start: 0.7693 (t0) cc_final: 0.7463 (t0) REVERT: B 523 HIS cc_start: 0.7712 (m-70) cc_final: 0.7285 (m-70) REVERT: B 555 MET cc_start: 0.8785 (ttp) cc_final: 0.8579 (ttm) REVERT: B 677 MET cc_start: 0.7496 (mtt) cc_final: 0.7240 (mtt) REVERT: B 679 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7238 (tp30) REVERT: B 722 LYS cc_start: 0.6623 (tttt) cc_final: 0.6412 (tttt) REVERT: C 119 LEU cc_start: 0.8550 (mm) cc_final: 0.8283 (mt) REVERT: C 121 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8483 (mtpt) REVERT: C 159 MET cc_start: 0.7668 (tpp) cc_final: 0.7370 (tpp) REVERT: C 249 PHE cc_start: 0.6262 (p90) cc_final: 0.4172 (m-80) REVERT: C 268 LEU cc_start: 0.8983 (pp) cc_final: 0.8759 (pp) REVERT: C 297 ASN cc_start: 0.7944 (m-40) cc_final: 0.7426 (m110) REVERT: C 335 THR cc_start: 0.9319 (p) cc_final: 0.8964 (t) REVERT: C 353 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8315 (mmtp) REVERT: C 540 TYR cc_start: 0.6552 (t80) cc_final: 0.6225 (t80) REVERT: C 555 MET cc_start: 0.8562 (ttm) cc_final: 0.8333 (ttm) REVERT: C 569 PHE cc_start: 0.8386 (m-80) cc_final: 0.8137 (m-10) REVERT: C 605 LEU cc_start: 0.9059 (mp) cc_final: 0.8575 (mt) REVERT: C 687 GLU cc_start: 0.6877 (tp30) cc_final: 0.6446 (pp20) REVERT: D 119 LEU cc_start: 0.8572 (mm) cc_final: 0.8290 (mt) REVERT: D 121 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8468 (mtpt) REVERT: D 159 MET cc_start: 0.7634 (tpp) cc_final: 0.7353 (tpp) REVERT: D 249 PHE cc_start: 0.6096 (p90) cc_final: 0.4075 (m-80) REVERT: D 268 LEU cc_start: 0.8990 (pp) cc_final: 0.8772 (pp) REVERT: D 297 ASN cc_start: 0.8171 (m110) cc_final: 0.7488 (m110) REVERT: D 335 THR cc_start: 0.9328 (p) cc_final: 0.8958 (t) REVERT: D 353 LYS cc_start: 0.9045 (mmtt) cc_final: 0.7989 (mmtp) REVERT: D 540 TYR cc_start: 0.6580 (t80) cc_final: 0.6246 (t80) REVERT: D 555 MET cc_start: 0.8533 (ttm) cc_final: 0.8319 (ttm) REVERT: D 562 MET cc_start: 0.8694 (ttt) cc_final: 0.8425 (ttt) REVERT: D 569 PHE cc_start: 0.8397 (m-80) cc_final: 0.8130 (m-10) REVERT: D 605 LEU cc_start: 0.9057 (mp) cc_final: 0.8614 (mt) REVERT: D 687 GLU cc_start: 0.6835 (tp30) cc_final: 0.6422 (pp20) REVERT: D 748 PHE cc_start: 0.7709 (p90) cc_final: 0.7497 (p90) outliers start: 1 outliers final: 0 residues processed: 607 average time/residue: 0.2768 time to fit residues: 269.3861 Evaluate side-chains 446 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 211 optimal weight: 0.0870 chunk 171 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 0.0670 overall best weight: 1.6302 ------------------------------------------------------------------------------- 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 452 ASN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21324 Z= 0.216 Angle : 0.749 11.642 28872 Z= 0.382 Chirality : 0.044 0.241 3308 Planarity : 0.005 0.079 3608 Dihedral : 6.286 35.725 2804 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.56 % Favored : 85.28 % Rotamer: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.77 % 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: -2.99 (0.15), residues: 2568 helix: -0.59 (0.13), residues: 1492 sheet: -5.68 (0.33), residues: 20 loop : -4.11 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 493 HIS 0.003 0.001 HIS A 417 PHE 0.022 0.002 PHE B 249 TYR 0.037 0.002 TYR B 650 ARG 0.002 0.000 ARG A 464 *********************** 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 574 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 570 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8711 (mm) cc_final: 0.8408 (mt) REVERT: A 159 MET cc_start: 0.7773 (tpp) cc_final: 0.7479 (tpp) REVERT: A 249 PHE cc_start: 0.6310 (p90) cc_final: 0.4185 (m-80) REVERT: A 268 LEU cc_start: 0.8932 (pp) cc_final: 0.8728 (pp) REVERT: A 297 ASN cc_start: 0.7891 (m-40) cc_final: 0.7568 (m110) REVERT: A 335 THR cc_start: 0.9313 (p) cc_final: 0.8936 (t) REVERT: A 353 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8468 (mmtm) REVERT: A 540 TYR cc_start: 0.6651 (t80) cc_final: 0.6243 (t80) REVERT: A 555 MET cc_start: 0.8584 (ttm) cc_final: 0.8337 (ttm) REVERT: A 562 MET cc_start: 0.8738 (ttt) cc_final: 0.8499 (ttt) REVERT: A 677 MET cc_start: 0.7792 (mtt) cc_final: 0.7484 (mtt) REVERT: A 687 GLU cc_start: 0.6776 (tp30) cc_final: 0.6408 (pp20) REVERT: A 748 PHE cc_start: 0.7739 (p90) cc_final: 0.7504 (p90) REVERT: B 119 LEU cc_start: 0.8663 (mm) cc_final: 0.8414 (mt) REVERT: B 121 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8374 (mtpt) REVERT: B 129 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 139 LEU cc_start: 0.9033 (mm) cc_final: 0.8805 (tp) REVERT: B 159 MET cc_start: 0.7468 (tpp) cc_final: 0.6879 (tpp) REVERT: B 297 ASN cc_start: 0.8089 (m110) cc_final: 0.7686 (m110) REVERT: B 320 MET cc_start: 0.8686 (mmm) cc_final: 0.8372 (mmm) REVERT: B 335 THR cc_start: 0.9253 (p) cc_final: 0.8802 (t) REVERT: B 479 MET cc_start: -0.0803 (mmm) cc_final: -0.1031 (mmm) REVERT: B 562 MET cc_start: 0.8800 (ttt) cc_final: 0.8490 (ttt) REVERT: B 677 MET cc_start: 0.7497 (mtt) cc_final: 0.7230 (mtt) REVERT: B 679 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7322 (tp30) REVERT: C 119 LEU cc_start: 0.8690 (mm) cc_final: 0.8384 (mt) REVERT: C 159 MET cc_start: 0.7723 (tpp) cc_final: 0.7408 (tpp) REVERT: C 249 PHE cc_start: 0.6269 (p90) cc_final: 0.4140 (m-80) REVERT: C 268 LEU cc_start: 0.8970 (pp) cc_final: 0.8765 (pp) REVERT: C 297 ASN cc_start: 0.7915 (m-40) cc_final: 0.7557 (m110) REVERT: C 335 THR cc_start: 0.9312 (p) cc_final: 0.8938 (t) REVERT: C 351 MET cc_start: 0.8224 (mmm) cc_final: 0.8020 (mmm) REVERT: C 353 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8449 (mmtm) REVERT: C 540 TYR cc_start: 0.6665 (t80) cc_final: 0.6254 (t80) REVERT: C 555 MET cc_start: 0.8641 (ttm) cc_final: 0.8419 (ttm) REVERT: C 687 GLU cc_start: 0.6814 (tp30) cc_final: 0.6373 (pp20) REVERT: D 119 LEU cc_start: 0.8701 (mm) cc_final: 0.8397 (mt) REVERT: D 159 MET cc_start: 0.7688 (tpp) cc_final: 0.7390 (tpp) REVERT: D 249 PHE cc_start: 0.6122 (p90) cc_final: 0.3973 (m-10) REVERT: D 268 LEU cc_start: 0.8952 (pp) cc_final: 0.8751 (pp) REVERT: D 297 ASN cc_start: 0.8176 (m110) cc_final: 0.7632 (m110) REVERT: D 335 THR cc_start: 0.9310 (p) cc_final: 0.8930 (t) REVERT: D 351 MET cc_start: 0.8242 (mmm) cc_final: 0.8018 (mmm) REVERT: D 353 LYS cc_start: 0.9146 (mmtt) cc_final: 0.8444 (mmtp) REVERT: D 540 TYR cc_start: 0.6693 (t80) cc_final: 0.6281 (t80) REVERT: D 555 MET cc_start: 0.8641 (ttm) cc_final: 0.8421 (ttm) REVERT: D 562 MET cc_start: 0.8731 (ttt) cc_final: 0.8490 (ttt) REVERT: D 687 GLU cc_start: 0.6842 (tp30) cc_final: 0.6405 (pp20) REVERT: D 748 PHE cc_start: 0.7778 (p90) cc_final: 0.7543 (p90) outliers start: 4 outliers final: 4 residues processed: 574 average time/residue: 0.2722 time to fit residues: 252.3810 Evaluate side-chains 420 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 247 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21324 Z= 0.225 Angle : 0.745 12.063 28872 Z= 0.381 Chirality : 0.046 0.393 3308 Planarity : 0.004 0.069 3608 Dihedral : 6.080 37.355 2804 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.52 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (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: -2.74 (0.16), residues: 2568 helix: -0.36 (0.13), residues: 1492 sheet: -5.50 (0.34), residues: 20 loop : -4.05 (0.15), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 493 HIS 0.003 0.001 HIS D 417 PHE 0.021 0.001 PHE B 249 TYR 0.023 0.002 TYR A 213 ARG 0.005 0.000 ARG D 464 *********************** 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 547 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8538 (mm) cc_final: 0.8316 (mt) REVERT: A 159 MET cc_start: 0.7740 (tpp) cc_final: 0.7466 (tpp) REVERT: A 249 PHE cc_start: 0.6324 (p90) cc_final: 0.4240 (m-80) REVERT: A 297 ASN cc_start: 0.7958 (m-40) cc_final: 0.7666 (m110) REVERT: A 335 THR cc_start: 0.9308 (p) cc_final: 0.8955 (t) REVERT: A 410 ASN cc_start: 0.7648 (t0) cc_final: 0.7420 (t0) REVERT: A 540 TYR cc_start: 0.6565 (t80) cc_final: 0.6227 (t80) REVERT: A 555 MET cc_start: 0.8641 (ttm) cc_final: 0.8326 (ttm) REVERT: A 562 MET cc_start: 0.8747 (ttt) cc_final: 0.8497 (ttt) REVERT: A 569 PHE cc_start: 0.8044 (m-80) cc_final: 0.7818 (m-10) REVERT: A 677 MET cc_start: 0.7704 (mtt) cc_final: 0.7456 (mtt) REVERT: A 687 GLU cc_start: 0.6788 (tp30) cc_final: 0.6349 (pp20) REVERT: A 722 LYS cc_start: 0.6599 (tttt) cc_final: 0.6309 (tttt) REVERT: B 119 LEU cc_start: 0.8645 (mm) cc_final: 0.8408 (mt) REVERT: B 129 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7622 (tm-30) REVERT: B 139 LEU cc_start: 0.9049 (mm) cc_final: 0.8842 (tp) REVERT: B 159 MET cc_start: 0.7482 (tpp) cc_final: 0.6871 (tpp) REVERT: B 297 ASN cc_start: 0.8077 (m110) cc_final: 0.7629 (m110) REVERT: B 335 THR cc_start: 0.9278 (p) cc_final: 0.8817 (t) REVERT: B 562 MET cc_start: 0.8802 (ttt) cc_final: 0.8566 (ttt) REVERT: B 569 PHE cc_start: 0.8105 (m-10) cc_final: 0.7871 (m-10) REVERT: B 679 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7445 (tp30) REVERT: C 119 LEU cc_start: 0.8499 (mm) cc_final: 0.8290 (mt) REVERT: C 159 MET cc_start: 0.7720 (tpp) cc_final: 0.7415 (tpp) REVERT: C 249 PHE cc_start: 0.6385 (p90) cc_final: 0.4310 (m-80) REVERT: C 297 ASN cc_start: 0.7979 (m-40) cc_final: 0.7655 (m110) REVERT: C 335 THR cc_start: 0.9296 (p) cc_final: 0.8944 (t) REVERT: C 410 ASN cc_start: 0.7653 (t0) cc_final: 0.7427 (t0) REVERT: C 540 TYR cc_start: 0.6581 (t80) cc_final: 0.6242 (t80) REVERT: C 555 MET cc_start: 0.8694 (ttm) cc_final: 0.8415 (ttm) REVERT: C 569 PHE cc_start: 0.8037 (m-80) cc_final: 0.7809 (m-10) REVERT: C 687 GLU cc_start: 0.6843 (tp30) cc_final: 0.6351 (pp20) REVERT: D 119 LEU cc_start: 0.8532 (mm) cc_final: 0.8305 (mt) REVERT: D 159 MET cc_start: 0.7733 (tpp) cc_final: 0.7435 (tpp) REVERT: D 249 PHE cc_start: 0.6336 (p90) cc_final: 0.4396 (m-80) REVERT: D 297 ASN cc_start: 0.8198 (m110) cc_final: 0.7411 (m110) REVERT: D 335 THR cc_start: 0.9306 (p) cc_final: 0.8950 (t) REVERT: D 410 ASN cc_start: 0.7638 (t0) cc_final: 0.7399 (t0) REVERT: D 540 TYR cc_start: 0.6613 (t80) cc_final: 0.6268 (t80) REVERT: D 555 MET cc_start: 0.8662 (ttm) cc_final: 0.8370 (ttm) REVERT: D 562 MET cc_start: 0.8724 (ttt) cc_final: 0.8491 (ttt) REVERT: D 569 PHE cc_start: 0.8049 (m-80) cc_final: 0.7820 (m-10) REVERT: D 687 GLU cc_start: 0.6828 (tp30) cc_final: 0.6337 (pp20) REVERT: D 722 LYS cc_start: 0.6610 (tttt) cc_final: 0.6363 (tttt) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.2629 time to fit residues: 233.7380 Evaluate side-chains 403 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 0.4980 chunk 138 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 314 ASN C 735 ASN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 735 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21324 Z= 0.182 Angle : 0.737 12.306 28872 Z= 0.372 Chirality : 0.044 0.313 3308 Planarity : 0.004 0.067 3608 Dihedral : 5.958 36.500 2804 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.37 % Favored : 85.48 % Rotamer: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % 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: -2.48 (0.16), residues: 2568 helix: -0.03 (0.14), residues: 1440 sheet: -4.66 (0.40), residues: 40 loop : -3.95 (0.15), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 493 HIS 0.003 0.001 HIS B 301 PHE 0.018 0.001 PHE B 506 TYR 0.021 0.001 TYR A 213 ARG 0.002 0.000 ARG C 464 *********************** 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 563 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 562 time to evaluate : 2.402 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: 0.8688 (mm) cc_final: 0.8452 (mt) REVERT: A 159 MET cc_start: 0.7714 (tpp) cc_final: 0.6890 (tpp) REVERT: A 163 THR cc_start: 0.8481 (m) cc_final: 0.8253 (p) REVERT: A 216 GLN cc_start: 0.8403 (tt0) cc_final: 0.8005 (mt0) REVERT: A 249 PHE cc_start: 0.6198 (p90) cc_final: 0.4288 (m-80) REVERT: A 297 ASN cc_start: 0.8006 (m-40) cc_final: 0.7672 (m110) REVERT: A 335 THR cc_start: 0.9284 (p) cc_final: 0.8912 (t) REVERT: A 540 TYR cc_start: 0.6556 (t80) cc_final: 0.6222 (t80) REVERT: A 555 MET cc_start: 0.8637 (ttm) cc_final: 0.8352 (ttm) REVERT: A 562 MET cc_start: 0.8747 (ttt) cc_final: 0.8524 (ttt) REVERT: A 569 PHE cc_start: 0.8056 (m-80) cc_final: 0.7853 (m-10) REVERT: A 677 MET cc_start: 0.7566 (mtt) cc_final: 0.7326 (mtt) REVERT: A 687 GLU cc_start: 0.6620 (tp30) cc_final: 0.6286 (pp20) REVERT: A 735 ASN cc_start: 0.9008 (m-40) cc_final: 0.8711 (m-40) REVERT: B 119 LEU cc_start: 0.8631 (mm) cc_final: 0.8402 (mt) REVERT: B 129 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 135 LEU cc_start: 0.8727 (tp) cc_final: 0.8517 (tp) REVERT: B 159 MET cc_start: 0.7398 (tpp) cc_final: 0.6790 (tpp) REVERT: B 297 ASN cc_start: 0.8101 (m110) cc_final: 0.7562 (m110) REVERT: B 335 THR cc_start: 0.9279 (p) cc_final: 0.8796 (t) REVERT: B 500 LYS cc_start: 0.6170 (ttpt) cc_final: 0.5750 (tptt) REVERT: B 562 MET cc_start: 0.8804 (ttt) cc_final: 0.8540 (ttt) REVERT: C 119 LEU cc_start: 0.8662 (mm) cc_final: 0.8427 (mt) REVERT: C 159 MET cc_start: 0.7708 (tpp) cc_final: 0.7403 (tpp) REVERT: C 249 PHE cc_start: 0.6243 (p90) cc_final: 0.4201 (m-80) REVERT: C 297 ASN cc_start: 0.7972 (m-40) cc_final: 0.7624 (m110) REVERT: C 335 THR cc_start: 0.9286 (p) cc_final: 0.8904 (t) REVERT: C 540 TYR cc_start: 0.6573 (t80) cc_final: 0.6244 (t80) REVERT: C 555 MET cc_start: 0.8657 (ttm) cc_final: 0.8390 (ttm) REVERT: C 687 GLU cc_start: 0.6524 (tp30) cc_final: 0.6175 (pp20) REVERT: C 722 LYS cc_start: 0.6678 (tttt) cc_final: 0.5836 (tppt) REVERT: D 119 LEU cc_start: 0.8684 (mm) cc_final: 0.8433 (mt) REVERT: D 159 MET cc_start: 0.7706 (tpp) cc_final: 0.6893 (tpp) REVERT: D 163 THR cc_start: 0.8488 (m) cc_final: 0.8275 (p) REVERT: D 216 GLN cc_start: 0.8435 (tt0) cc_final: 0.8009 (mt0) REVERT: D 249 PHE cc_start: 0.6193 (p90) cc_final: 0.4291 (m-80) REVERT: D 335 THR cc_start: 0.9284 (p) cc_final: 0.8904 (t) REVERT: D 540 TYR cc_start: 0.6603 (t80) cc_final: 0.6261 (t80) REVERT: D 555 MET cc_start: 0.8634 (ttm) cc_final: 0.8369 (ttm) REVERT: D 562 MET cc_start: 0.8730 (ttt) cc_final: 0.8503 (ttt) REVERT: D 569 PHE cc_start: 0.8058 (m-80) cc_final: 0.7853 (m-10) REVERT: D 687 GLU cc_start: 0.6554 (tp30) cc_final: 0.6168 (pp20) REVERT: D 722 LYS cc_start: 0.6654 (tttt) cc_final: 0.6416 (tttt) REVERT: D 735 ASN cc_start: 0.8987 (m-40) cc_final: 0.8712 (m-40) outliers start: 1 outliers final: 0 residues processed: 563 average time/residue: 0.2784 time to fit residues: 251.6507 Evaluate side-chains 419 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 0.0000 chunk 147 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21324 Z= 0.176 Angle : 0.733 12.487 28872 Z= 0.367 Chirality : 0.045 0.465 3308 Planarity : 0.004 0.066 3608 Dihedral : 5.747 36.723 2804 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.63 % Favored : 86.21 % Rotamer: Outliers : 0.04 % Allowed : 1.85 % Favored : 98.10 % 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: 0.25 (0.14), residues: 1444 sheet: -3.91 (0.36), residues: 72 loop : -3.90 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 481 HIS 0.004 0.001 HIS D 301 PHE 0.018 0.001 PHE A 506 TYR 0.022 0.001 TYR B 213 ARG 0.003 0.000 ARG D 464 *********************** 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 549 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8678 (mm) cc_final: 0.8444 (mt) REVERT: A 159 MET cc_start: 0.7657 (tpp) cc_final: 0.6813 (tpp) REVERT: A 163 THR cc_start: 0.8405 (m) cc_final: 0.8190 (p) REVERT: A 216 GLN cc_start: 0.8340 (tt0) cc_final: 0.8031 (mt0) REVERT: A 249 PHE cc_start: 0.6119 (p90) cc_final: 0.4173 (m-80) REVERT: A 335 THR cc_start: 0.9288 (p) cc_final: 0.8909 (t) REVERT: A 540 TYR cc_start: 0.6500 (t80) cc_final: 0.6201 (t80) REVERT: A 555 MET cc_start: 0.8606 (ttm) cc_final: 0.8371 (ttm) REVERT: A 562 MET cc_start: 0.8766 (ttt) cc_final: 0.8519 (ttt) REVERT: A 569 PHE cc_start: 0.8136 (m-80) cc_final: 0.7886 (m-10) REVERT: A 722 LYS cc_start: 0.6366 (tttt) cc_final: 0.5670 (tppt) REVERT: B 119 LEU cc_start: 0.8637 (mm) cc_final: 0.8399 (mt) REVERT: B 129 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7543 (tm-30) REVERT: B 159 MET cc_start: 0.7519 (tpp) cc_final: 0.6904 (tpp) REVERT: B 290 THR cc_start: 0.8514 (m) cc_final: 0.8191 (t) REVERT: B 297 ASN cc_start: 0.8041 (m110) cc_final: 0.7605 (m110) REVERT: B 335 THR cc_start: 0.9271 (p) cc_final: 0.8793 (t) REVERT: B 500 LYS cc_start: 0.5929 (ttpt) cc_final: 0.5580 (tptt) REVERT: B 562 MET cc_start: 0.8766 (ttt) cc_final: 0.8522 (ttt) REVERT: B 574 MET cc_start: 0.7990 (mpp) cc_final: 0.7783 (mpp) REVERT: B 679 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7454 (tp30) REVERT: C 119 LEU cc_start: 0.8663 (mm) cc_final: 0.8441 (mt) REVERT: C 159 MET cc_start: 0.7677 (tpp) cc_final: 0.7375 (tpp) REVERT: C 249 PHE cc_start: 0.6123 (p90) cc_final: 0.4216 (m-80) REVERT: C 297 ASN cc_start: 0.7860 (m-40) cc_final: 0.7652 (m110) REVERT: C 335 THR cc_start: 0.9285 (p) cc_final: 0.8900 (t) REVERT: C 506 PHE cc_start: 0.7886 (t80) cc_final: 0.7672 (t80) REVERT: C 540 TYR cc_start: 0.6532 (t80) cc_final: 0.6218 (t80) REVERT: C 555 MET cc_start: 0.8628 (ttm) cc_final: 0.8377 (ttm) REVERT: C 687 GLU cc_start: 0.6363 (tp30) cc_final: 0.6085 (pp20) REVERT: C 722 LYS cc_start: 0.6507 (tttt) cc_final: 0.5669 (tppt) REVERT: D 119 LEU cc_start: 0.8675 (mm) cc_final: 0.8443 (mt) REVERT: D 159 MET cc_start: 0.7667 (tpp) cc_final: 0.6811 (tpp) REVERT: D 216 GLN cc_start: 0.8386 (tt0) cc_final: 0.8015 (mt0) REVERT: D 249 PHE cc_start: 0.6002 (p90) cc_final: 0.4076 (m-80) REVERT: D 335 THR cc_start: 0.9281 (p) cc_final: 0.8899 (t) REVERT: D 506 PHE cc_start: 0.7856 (t80) cc_final: 0.7637 (t80) REVERT: D 540 TYR cc_start: 0.6546 (t80) cc_final: 0.6239 (t80) REVERT: D 555 MET cc_start: 0.8604 (ttm) cc_final: 0.8358 (ttm) REVERT: D 562 MET cc_start: 0.8752 (ttt) cc_final: 0.8512 (ttt) REVERT: D 569 PHE cc_start: 0.8136 (m-80) cc_final: 0.7890 (m-10) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.2683 time to fit residues: 239.3048 Evaluate side-chains 413 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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: 8.9990 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 100 optimal weight: 0.0050 chunk 180 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5766 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= 0.179 Angle : 0.729 12.281 28872 Z= 0.366 Chirality : 0.044 0.372 3308 Planarity : 0.004 0.066 3608 Dihedral : 5.685 37.574 2804 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.67 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % 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: -2.07 (0.16), residues: 2568 helix: 0.34 (0.14), residues: 1440 sheet: -4.09 (0.50), residues: 40 loop : -3.84 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 739 HIS 0.003 0.001 HIS D 301 PHE 0.022 0.001 PHE A 506 TYR 0.021 0.001 TYR D 213 ARG 0.007 0.000 ARG D 733 *********************** 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 539 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 2.539 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: A 119 LEU cc_start: 0.8690 (mm) cc_final: 0.8448 (mt) REVERT: A 159 MET cc_start: 0.7708 (tpp) cc_final: 0.6838 (tpp) REVERT: A 163 THR cc_start: 0.8419 (m) cc_final: 0.8209 (p) REVERT: A 216 GLN cc_start: 0.8367 (tt0) cc_final: 0.7941 (mt0) REVERT: A 297 ASN cc_start: 0.8095 (m110) cc_final: 0.7738 (m110) REVERT: A 335 THR cc_start: 0.9296 (p) cc_final: 0.8915 (t) REVERT: A 479 MET cc_start: -0.0733 (mmm) cc_final: -0.1217 (mmm) REVERT: A 488 MET cc_start: 0.7207 (mtt) cc_final: 0.6686 (mmm) REVERT: A 540 TYR cc_start: 0.6489 (t80) cc_final: 0.6264 (t80) REVERT: A 555 MET cc_start: 0.8642 (ttm) cc_final: 0.8361 (ttm) REVERT: A 562 MET cc_start: 0.8777 (ttt) cc_final: 0.8540 (ttt) REVERT: A 569 PHE cc_start: 0.8156 (m-80) cc_final: 0.7900 (m-10) REVERT: A 722 LYS cc_start: 0.6484 (tttt) cc_final: 0.5643 (tptt) REVERT: B 119 LEU cc_start: 0.8598 (mm) cc_final: 0.8347 (mt) REVERT: B 129 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 159 MET cc_start: 0.7540 (tpp) cc_final: 0.6905 (tpp) REVERT: B 290 THR cc_start: 0.8468 (m) cc_final: 0.8127 (t) REVERT: B 297 ASN cc_start: 0.8089 (m110) cc_final: 0.7643 (m110) REVERT: B 335 THR cc_start: 0.9264 (p) cc_final: 0.8768 (t) REVERT: B 479 MET cc_start: -0.0894 (mmm) cc_final: -0.1181 (mmm) REVERT: B 562 MET cc_start: 0.8816 (ttt) cc_final: 0.8568 (ttt) REVERT: B 679 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7482 (tp30) REVERT: C 119 LEU cc_start: 0.8645 (mm) cc_final: 0.8428 (mt) REVERT: C 159 MET cc_start: 0.7755 (tpp) cc_final: 0.7462 (tpp) REVERT: C 216 GLN cc_start: 0.8661 (tt0) cc_final: 0.8204 (mt0) REVERT: C 249 PHE cc_start: 0.6212 (p90) cc_final: 0.4317 (m-80) REVERT: C 297 ASN cc_start: 0.7872 (m-40) cc_final: 0.7662 (m110) REVERT: C 335 THR cc_start: 0.9311 (p) cc_final: 0.8930 (t) REVERT: C 479 MET cc_start: -0.0691 (mmm) cc_final: -0.1164 (mmm) REVERT: C 488 MET cc_start: 0.7200 (mtt) cc_final: 0.6667 (mmm) REVERT: C 540 TYR cc_start: 0.6528 (t80) cc_final: 0.6281 (t80) REVERT: C 555 MET cc_start: 0.8659 (ttm) cc_final: 0.8402 (ttm) REVERT: C 569 PHE cc_start: 0.8077 (m-80) cc_final: 0.7824 (m-10) REVERT: C 722 LYS cc_start: 0.6493 (tttt) cc_final: 0.5676 (tppt) REVERT: C 735 ASN cc_start: 0.8996 (m-40) cc_final: 0.8578 (m-40) REVERT: C 748 PHE cc_start: 0.7807 (p90) cc_final: 0.7593 (p90) REVERT: D 119 LEU cc_start: 0.8680 (mm) cc_final: 0.8424 (mt) REVERT: D 216 GLN cc_start: 0.8357 (tt0) cc_final: 0.7915 (mt0) REVERT: D 249 PHE cc_start: 0.5956 (p90) cc_final: 0.4152 (m-80) REVERT: D 335 THR cc_start: 0.9285 (p) cc_final: 0.8906 (t) REVERT: D 479 MET cc_start: -0.0668 (mmm) cc_final: -0.1154 (mmm) REVERT: D 488 MET cc_start: 0.7183 (mtt) cc_final: 0.6653 (mmm) REVERT: D 540 TYR cc_start: 0.6556 (t80) cc_final: 0.6309 (t80) REVERT: D 555 MET cc_start: 0.8638 (ttm) cc_final: 0.8367 (ttm) REVERT: D 562 MET cc_start: 0.8770 (ttt) cc_final: 0.8536 (ttt) REVERT: D 569 PHE cc_start: 0.8159 (m-80) cc_final: 0.7883 (m-10) REVERT: D 722 LYS cc_start: 0.6388 (tttt) cc_final: 0.5700 (tppt) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.2843 time to fit residues: 248.5432 Evaluate side-chains 412 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.0010 chunk 148 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 161 optimal weight: 3.9990 overall best weight: 1.2110 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.5848 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= 0.197 Angle : 0.756 13.050 28872 Z= 0.376 Chirality : 0.044 0.287 3308 Planarity : 0.004 0.063 3608 Dihedral : 5.636 36.468 2804 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.43 % Favored : 86.41 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -2.04 (0.16), residues: 2568 helix: 0.40 (0.14), residues: 1444 sheet: -4.09 (0.41), residues: 60 loop : -3.87 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 739 HIS 0.005 0.001 HIS B 426 PHE 0.022 0.001 PHE D 506 TYR 0.024 0.002 TYR B 540 ARG 0.008 0.000 ARG D 733 ********************** 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 530 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 2.119 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: 0.8669 (mm) cc_final: 0.8434 (mt) REVERT: A 159 MET cc_start: 0.7667 (tpp) cc_final: 0.6800 (tpp) REVERT: A 163 THR cc_start: 0.8456 (m) cc_final: 0.8212 (p) REVERT: A 216 GLN cc_start: 0.8396 (tt0) cc_final: 0.7962 (mt0) REVERT: A 297 ASN cc_start: 0.8112 (m110) cc_final: 0.7690 (m110) REVERT: A 335 THR cc_start: 0.9310 (p) cc_final: 0.8938 (t) REVERT: A 479 MET cc_start: -0.1026 (mmm) cc_final: -0.1487 (mmm) REVERT: A 488 MET cc_start: 0.7276 (mtt) cc_final: 0.6766 (mmm) REVERT: A 555 MET cc_start: 0.8636 (ttm) cc_final: 0.8356 (ttm) REVERT: A 562 MET cc_start: 0.8745 (ttt) cc_final: 0.8522 (ttt) REVERT: A 569 PHE cc_start: 0.8156 (m-80) cc_final: 0.7901 (m-10) REVERT: A 722 LYS cc_start: 0.6520 (tttt) cc_final: 0.5567 (tptt) REVERT: A 748 PHE cc_start: 0.7782 (p90) cc_final: 0.7564 (p90) REVERT: B 119 LEU cc_start: 0.8624 (mm) cc_final: 0.8363 (mt) REVERT: B 129 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 159 MET cc_start: 0.7549 (tpp) cc_final: 0.6924 (tpp) REVERT: B 290 THR cc_start: 0.8467 (m) cc_final: 0.8121 (t) REVERT: B 297 ASN cc_start: 0.8075 (m110) cc_final: 0.7632 (m110) REVERT: B 335 THR cc_start: 0.9247 (p) cc_final: 0.8777 (t) REVERT: B 479 MET cc_start: -0.1089 (mmm) cc_final: -0.1514 (mmm) REVERT: B 562 MET cc_start: 0.8810 (ttt) cc_final: 0.8567 (ttt) REVERT: B 679 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7499 (tp30) REVERT: C 119 LEU cc_start: 0.8656 (mm) cc_final: 0.8437 (mt) REVERT: C 159 MET cc_start: 0.7753 (tpp) cc_final: 0.6881 (tpp) REVERT: C 163 THR cc_start: 0.8469 (m) cc_final: 0.8225 (p) REVERT: C 216 GLN cc_start: 0.8676 (tt0) cc_final: 0.8147 (mt0) REVERT: C 297 ASN cc_start: 0.7900 (m-40) cc_final: 0.7689 (m110) REVERT: C 335 THR cc_start: 0.9319 (p) cc_final: 0.8941 (t) REVERT: C 479 MET cc_start: -0.0984 (mmm) cc_final: -0.1448 (mmm) REVERT: C 488 MET cc_start: 0.7266 (mtt) cc_final: 0.6774 (mmm) REVERT: C 540 TYR cc_start: 0.6570 (t80) cc_final: 0.6336 (t80) REVERT: C 555 MET cc_start: 0.8652 (ttm) cc_final: 0.8404 (ttm) REVERT: C 569 PHE cc_start: 0.8050 (m-80) cc_final: 0.7810 (m-10) REVERT: C 722 LYS cc_start: 0.6486 (tttt) cc_final: 0.5441 (tptt) REVERT: D 119 LEU cc_start: 0.8667 (mm) cc_final: 0.8423 (mt) REVERT: D 159 MET cc_start: 0.8192 (mmp) cc_final: 0.7720 (tpp) REVERT: D 216 GLN cc_start: 0.8386 (tt0) cc_final: 0.8076 (mt0) REVERT: D 249 PHE cc_start: 0.6107 (p90) cc_final: 0.4269 (m-80) REVERT: D 335 THR cc_start: 0.9302 (p) cc_final: 0.8926 (t) REVERT: D 479 MET cc_start: -0.0983 (mmm) cc_final: -0.1434 (mmm) REVERT: D 488 MET cc_start: 0.7268 (mtt) cc_final: 0.6761 (mmm) REVERT: D 540 TYR cc_start: 0.6580 (t80) cc_final: 0.6363 (t80) REVERT: D 555 MET cc_start: 0.8632 (ttm) cc_final: 0.8384 (ttm) REVERT: D 562 MET cc_start: 0.8776 (ttt) cc_final: 0.8543 (ttt) REVERT: D 569 PHE cc_start: 0.8091 (m-80) cc_final: 0.7859 (m-10) REVERT: D 722 LYS cc_start: 0.6410 (tttt) cc_final: 0.5471 (tptt) REVERT: D 735 ASN cc_start: 0.8784 (m-40) cc_final: 0.8346 (m-40) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.2862 time to fit residues: 243.4444 Evaluate side-chains 405 residues out of total 2296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 0.0870 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 735 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 = 0.3658 r_free = 0.3658 target = 0.144068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114644 restraints weight = 35622.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117145 restraints weight = 24174.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118309 restraints weight = 18715.051| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21324 Z= 0.237 Angle : 0.775 12.926 28872 Z= 0.388 Chirality : 0.045 0.205 3308 Planarity : 0.004 0.062 3608 Dihedral : 5.651 33.873 2804 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.79 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -2.00 (0.17), residues: 2568 helix: 0.41 (0.14), residues: 1440 sheet: -3.77 (0.58), residues: 40 loop : -3.84 (0.16), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 481 HIS 0.003 0.001 HIS B 585 PHE 0.023 0.001 PHE A 506 TYR 0.037 0.002 TYR A 540 ARG 0.006 0.000 ARG D 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.20 seconds wall clock time: 88 minutes 24.37 seconds (5304.37 seconds total)