Starting phenix.real_space_refine on Sat Sep 28 17:29:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aa5_11690/09_2024/7aa5_11690_neut.cif" } resolution = 4.18 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= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 108 5.16 5 C 12804 2.51 5 N 3268 2.21 5 O 3516 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 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: 19705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "B" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "D" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.04, per 1000 atoms: 0.71 Number of scatterers: 19705 At special positions: 0 Unit cell: (147.609, 147.609, 116.937, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 108 16.00 O 3516 8.00 N 3268 7.00 C 12804 6.00 H 8 1.00 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: 5.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 61.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.999A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.736A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 4.119A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.546A pdb=" N SER A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.897A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.625A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 635 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 729 through 748 removed outlier: 3.638A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.735A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.692A pdb=" N THR B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 635 Processing helix chain 'B' and resid 667 through 678 Processing helix chain 'B' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP C 165 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.698A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 400' Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 570 removed outlier: 3.545A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 635 Processing helix chain 'C' and resid 667 through 678 Processing helix chain 'C' and resid 693 through 709 removed outlier: 4.255A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 698 " --> pdb=" O VAL C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 722 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR D 399 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 400' Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 530 removed outlier: 3.553A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER D 557 " --> pdb=" O TYR D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU D 598 " --> pdb=" O GLY D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 635 Processing helix chain 'D' and resid 667 through 678 Processing helix chain 'D' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 698 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 722 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU A 418 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.652A pdb=" N LEU B 418 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU C 418 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU D 418 " --> pdb=" O PHE D 406 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2784 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: 5.75 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 8 1.17 - 1.33: 4161 1.33 - 1.49: 7284 1.49 - 1.65: 8513 1.65 - 1.81: 178 Bond restraints: 20144 Sorted by residual: bond pdb=" N PRO D 772 " pdb=" CD PRO D 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO B 772 " pdb=" CD PRO B 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.91e+02 bond pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.90e+02 bond pdb=" N PRO C 772 " pdb=" CD PRO C 772 " ideal model delta sigma weight residual 1.473 1.629 -0.156 1.40e-02 5.10e+03 1.25e+02 ... (remaining 20139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.99: 27222 5.99 - 11.97: 62 11.97 - 17.96: 5 17.96 - 23.94: 6 23.94 - 29.93: 1 Bond angle restraints: 27296 Sorted by residual: angle pdb=" C THR C 771 " pdb=" N PRO C 772 " pdb=" CA PRO C 772 " ideal model delta sigma weight residual 119.84 99.71 20.13 1.25e+00 6.40e-01 2.59e+02 angle pdb=" CA THR B 771 " pdb=" C THR B 771 " pdb=" O THR B 771 " ideal model delta sigma weight residual 120.16 100.91 19.25 1.37e+00 5.33e-01 1.97e+02 angle pdb=" CA THR D 771 " pdb=" C THR D 771 " pdb=" O THR D 771 " ideal model delta sigma weight residual 120.16 100.93 19.23 1.37e+00 5.33e-01 1.97e+02 angle pdb=" C THR D 771 " pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 119.84 102.33 17.51 1.25e+00 6.40e-01 1.96e+02 angle pdb=" C THR B 771 " pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 119.84 102.34 17.50 1.25e+00 6.40e-01 1.96e+02 ... (remaining 27291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10620 17.58 - 35.16: 1116 35.16 - 52.73: 209 52.73 - 70.31: 46 70.31 - 87.89: 9 Dihedral angle restraints: 12000 sinusoidal: 4820 harmonic: 7180 Sorted by residual: dihedral pdb=" CA GLY C 770 " pdb=" C GLY C 770 " pdb=" N THR C 771 " pdb=" CA THR C 771 " ideal model delta harmonic sigma weight residual 180.00 106.78 73.22 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLY D 770 " pdb=" C GLY D 770 " pdb=" N THR D 771 " pdb=" CA THR D 771 " ideal model delta harmonic sigma weight residual 180.00 122.37 57.63 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA GLY B 770 " pdb=" C GLY B 770 " pdb=" N THR B 771 " pdb=" CA THR B 771 " ideal model delta harmonic sigma weight residual 180.00 122.41 57.59 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 11997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3052 0.095 - 0.190: 78 0.190 - 0.286: 2 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO B 772 " pdb=" N PRO B 772 " pdb=" C PRO B 772 " pdb=" CB PRO B 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA PRO D 772 " pdb=" N PRO D 772 " pdb=" C PRO D 772 " pdb=" CB PRO D 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB THR A 771 " pdb=" CA THR A 771 " pdb=" OG1 THR A 771 " pdb=" CG2 THR A 771 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 3133 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " 0.024 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLY A 770 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 770 " 0.037 2.00e-02 2.50e+03 pdb=" N THR A 771 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 771 " -0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C THR B 771 " 0.075 2.00e-02 2.50e+03 pdb=" O THR B 771 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO B 772 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 771 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR D 771 " -0.075 2.00e-02 2.50e+03 pdb=" O THR D 771 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO D 772 " 0.028 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.62: 403 2.62 - 3.11: 17172 3.11 - 3.61: 25393 3.61 - 4.10: 32478 4.10 - 4.60: 47585 Nonbonded interactions: 123031 Sorted by model distance: nonbonded pdb=" O THR A 339 " pdb=" OG1 THR A 343 " model vdw 2.119 2.800 nonbonded pdb=" O THR B 339 " pdb=" OG1 THR B 343 " model vdw 2.120 2.800 nonbonded pdb=" O THR C 339 " pdb=" OG1 THR C 343 " model vdw 2.120 2.800 nonbonded pdb=" O THR D 339 " pdb=" OG1 THR D 343 " model vdw 2.120 2.800 nonbonded pdb=" O ALA D 217 " pdb=" OG1 THR D 220 " model vdw 2.199 2.800 ... (remaining 123026 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 148 through 786) selection = chain 'B' 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: 12.140 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: 0.500 Extract box with map and model: 0.860 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 46.450 Find NCS groups from input model: 0.820 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.241 20136 Z= 0.392 Angle : 0.921 29.930 27288 Z= 0.544 Chirality : 0.045 0.476 3136 Planarity : 0.005 0.072 3408 Dihedral : 14.673 87.890 7360 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.06 % Favored : 84.74 % Rotamer: Outliers : 2.04 % Allowed : 4.72 % Favored : 93.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.34 % 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: -4.78 (0.13), residues: 2424 helix: -2.43 (0.11), residues: 1336 sheet: -1.80 (0.54), residues: 76 loop : -4.33 (0.15), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 733 HIS 0.004 0.001 HIS C 326 PHE 0.012 0.001 PHE B 756 TYR 0.012 0.001 TYR C 500 ARG 0.004 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 2.348 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 223 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: A 482 MET cc_start: 0.8206 (mmm) cc_final: 0.7707 (mmt) REVERT: A 578 MET cc_start: 0.6533 (mtp) cc_final: 0.6286 (tpp) REVERT: A 757 ARG cc_start: 0.8177 (ppt170) cc_final: 0.7956 (ppt170) REVERT: B 176 HIS cc_start: 0.8619 (t-170) cc_final: 0.8132 (m90) REVERT: B 482 MET cc_start: 0.7450 (mmm) cc_final: 0.6929 (mmt) REVERT: B 556 TYR cc_start: 0.9269 (t80) cc_final: 0.8726 (t80) REVERT: B 761 MET cc_start: 0.8316 (mmp) cc_final: 0.8035 (mmp) REVERT: C 223 MET cc_start: 0.7257 (mmm) cc_final: 0.6986 (mmm) REVERT: C 225 GLU cc_start: 0.7495 (tt0) cc_final: 0.7281 (tt0) REVERT: C 482 MET cc_start: 0.8305 (mmm) cc_final: 0.7802 (mmt) REVERT: D 223 MET cc_start: 0.7133 (mmm) cc_final: 0.6838 (mmm) REVERT: D 225 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (tt0) REVERT: D 482 MET cc_start: 0.8211 (mmm) cc_final: 0.7717 (mmt) REVERT: D 713 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9099 (mmt) REVERT: D 757 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7976 (ppt170) outliers start: 44 outliers final: 19 residues processed: 280 average time/residue: 0.2915 time to fit residues: 127.3327 Evaluate side-chains 205 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 221 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 326 HIS ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 326 HIS ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 326 HIS ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20136 Z= 0.290 Angle : 0.666 8.737 27288 Z= 0.350 Chirality : 0.039 0.155 3136 Planarity : 0.004 0.044 3408 Dihedral : 5.943 41.615 2692 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 50.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.81 % Favored : 85.02 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.15), residues: 2424 helix: -0.78 (0.13), residues: 1368 sheet: -1.68 (0.53), residues: 76 loop : -4.13 (0.16), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.006 0.001 HIS B 326 PHE 0.056 0.002 PHE B 615 TYR 0.015 0.002 TYR B 303 ARG 0.004 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.096 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 176 HIS cc_start: 0.9031 (t-90) cc_final: 0.8131 (t-90) REVERT: A 178 LYS cc_start: 0.8768 (mmmt) cc_final: 0.8505 (mmmt) REVERT: A 397 GLU cc_start: 0.8903 (pm20) cc_final: 0.8474 (tm-30) REVERT: A 482 MET cc_start: 0.8215 (mmm) cc_final: 0.7898 (mmt) REVERT: A 578 MET cc_start: 0.6586 (mtp) cc_final: 0.6320 (mtt) REVERT: A 587 MET cc_start: 0.8967 (mtm) cc_final: 0.8724 (mtp) REVERT: A 624 PHE cc_start: 0.9155 (m-80) cc_final: 0.8879 (m-80) REVERT: B 578 MET cc_start: 0.4672 (mtt) cc_final: 0.4439 (tpp) REVERT: B 587 MET cc_start: 0.8765 (mtm) cc_final: 0.8408 (mtp) REVERT: B 624 PHE cc_start: 0.9088 (m-80) cc_final: 0.8798 (m-80) REVERT: C 176 HIS cc_start: 0.9052 (t-90) cc_final: 0.8186 (t-90) REVERT: C 178 LYS cc_start: 0.8674 (mmmt) cc_final: 0.8453 (mmmt) REVERT: C 397 GLU cc_start: 0.8869 (pm20) cc_final: 0.8416 (tm-30) REVERT: C 587 MET cc_start: 0.8972 (mtm) cc_final: 0.8736 (mtp) REVERT: C 624 PHE cc_start: 0.9083 (m-80) cc_final: 0.8873 (m-80) REVERT: D 176 HIS cc_start: 0.9081 (t-90) cc_final: 0.8219 (t-90) REVERT: D 178 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8513 (mmmt) REVERT: D 397 GLU cc_start: 0.8903 (pm20) cc_final: 0.8504 (tm-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3138 time to fit residues: 110.3548 Evaluate side-chains 186 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20136 Z= 0.299 Angle : 0.653 7.550 27288 Z= 0.343 Chirality : 0.038 0.156 3136 Planarity : 0.004 0.038 3408 Dihedral : 5.772 36.522 2692 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 62.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.22 % Favored : 84.61 % Rotamer: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.77 (0.16), residues: 2424 helix: -0.38 (0.13), residues: 1396 sheet: -1.37 (0.55), residues: 76 loop : -4.27 (0.16), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 586 HIS 0.008 0.002 HIS C 731 PHE 0.020 0.002 PHE A 778 TYR 0.023 0.002 TYR C 303 ARG 0.013 0.001 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.448 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 176 HIS cc_start: 0.9100 (t-90) cc_final: 0.8808 (t-90) REVERT: A 587 MET cc_start: 0.8954 (mtm) cc_final: 0.8731 (mtp) REVERT: A 624 PHE cc_start: 0.9133 (m-80) cc_final: 0.8857 (m-80) REVERT: A 761 MET cc_start: 0.8392 (mmp) cc_final: 0.7957 (mmp) REVERT: B 176 HIS cc_start: 0.9011 (t-90) cc_final: 0.8235 (t-90) REVERT: B 178 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8556 (mmmt) REVERT: B 219 ARG cc_start: 0.8017 (mmt90) cc_final: 0.7735 (mmt90) REVERT: B 587 MET cc_start: 0.8824 (mtm) cc_final: 0.8528 (mtp) REVERT: B 624 PHE cc_start: 0.9066 (m-80) cc_final: 0.8821 (m-80) REVERT: B 761 MET cc_start: 0.8368 (mmp) cc_final: 0.8137 (mmp) REVERT: C 176 HIS cc_start: 0.9059 (t-90) cc_final: 0.8774 (t-90) REVERT: C 624 PHE cc_start: 0.9094 (m-80) cc_final: 0.8881 (m-80) REVERT: C 761 MET cc_start: 0.8441 (mmp) cc_final: 0.8148 (mmp) REVERT: D 176 HIS cc_start: 0.9081 (t-90) cc_final: 0.8806 (t-90) REVERT: D 587 MET cc_start: 0.8901 (mtm) cc_final: 0.8628 (mtp) REVERT: D 624 PHE cc_start: 0.9042 (m-80) cc_final: 0.8835 (m-80) REVERT: D 625 MET cc_start: 0.8952 (ptp) cc_final: 0.8602 (ptp) REVERT: D 761 MET cc_start: 0.8378 (mmp) cc_final: 0.8106 (mmp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3128 time to fit residues: 107.6371 Evaluate side-chains 179 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20136 Z= 0.379 Angle : 0.749 7.910 27288 Z= 0.386 Chirality : 0.041 0.213 3136 Planarity : 0.005 0.059 3408 Dihedral : 5.963 35.103 2692 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 72.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 17.86 % Favored : 81.97 % Rotamer: Outliers : 0.14 % Allowed : 5.46 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.90 (0.16), residues: 2424 helix: -0.45 (0.13), residues: 1396 sheet: -1.24 (0.56), residues: 76 loop : -4.41 (0.16), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 586 HIS 0.008 0.002 HIS A 326 PHE 0.022 0.002 PHE B 778 TYR 0.033 0.002 TYR C 303 ARG 0.005 0.001 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 213 time to evaluate : 2.315 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: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9126 (t-90) cc_final: 0.8770 (t-90) REVERT: A 368 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8934 (m-40) REVERT: A 449 MET cc_start: 0.9137 (mtt) cc_final: 0.8898 (mtt) REVERT: A 587 MET cc_start: 0.8935 (mtm) cc_final: 0.8731 (mtp) REVERT: A 624 PHE cc_start: 0.9180 (m-80) cc_final: 0.8901 (m-80) REVERT: A 761 MET cc_start: 0.8336 (mmp) cc_final: 0.7770 (mmp) REVERT: B 176 HIS cc_start: 0.9118 (t-90) cc_final: 0.8818 (t-90) REVERT: B 219 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7673 (mmt90) REVERT: B 587 MET cc_start: 0.8805 (mtm) cc_final: 0.8494 (mtp) REVERT: B 624 PHE cc_start: 0.9125 (m-80) cc_final: 0.8838 (m-80) REVERT: B 642 MET cc_start: 0.8759 (tpt) cc_final: 0.8524 (tpp) REVERT: B 685 MET cc_start: 0.1726 (tpt) cc_final: 0.1405 (tpt) REVERT: B 761 MET cc_start: 0.8404 (mmp) cc_final: 0.8127 (mmp) REVERT: C 176 HIS cc_start: 0.9130 (t-90) cc_final: 0.8776 (t-90) REVERT: C 622 LEU cc_start: 0.9247 (tp) cc_final: 0.9021 (tp) REVERT: C 624 PHE cc_start: 0.9104 (m-80) cc_final: 0.8865 (m-80) REVERT: C 685 MET cc_start: 0.1540 (tpt) cc_final: 0.1218 (tpt) REVERT: C 761 MET cc_start: 0.8365 (mmp) cc_final: 0.8095 (mmp) REVERT: D 176 HIS cc_start: 0.9131 (t-90) cc_final: 0.8802 (t-90) REVERT: D 368 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8935 (m-40) REVERT: D 587 MET cc_start: 0.8915 (mtm) cc_final: 0.8639 (mtp) REVERT: D 624 PHE cc_start: 0.9138 (m-80) cc_final: 0.8886 (m-80) REVERT: D 761 MET cc_start: 0.8327 (mmp) cc_final: 0.8082 (mmp) outliers start: 3 outliers final: 0 residues processed: 216 average time/residue: 0.3105 time to fit residues: 104.6722 Evaluate side-chains 182 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 0.0270 chunk 211 optimal weight: 10.0000 chunk 59 optimal weight: 0.0370 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN B 401 HIS ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20136 Z= 0.177 Angle : 0.540 5.850 27288 Z= 0.287 Chirality : 0.036 0.133 3136 Planarity : 0.004 0.048 3408 Dihedral : 5.355 31.765 2692 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 60.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.24 % Favored : 86.59 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.20 (0.17), residues: 2424 helix: 0.16 (0.14), residues: 1396 sheet: -1.01 (0.58), residues: 76 loop : -4.17 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 586 HIS 0.004 0.001 HIS B 401 PHE 0.017 0.001 PHE D 624 TYR 0.014 0.001 TYR A 628 ARG 0.003 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9094 (t-90) cc_final: 0.8771 (t-90) REVERT: A 397 GLU cc_start: 0.8928 (pm20) cc_final: 0.8523 (tm-30) REVERT: A 624 PHE cc_start: 0.9106 (m-80) cc_final: 0.8853 (m-80) REVERT: A 761 MET cc_start: 0.8266 (mmp) cc_final: 0.7921 (mmp) REVERT: B 176 HIS cc_start: 0.9047 (t-90) cc_final: 0.8791 (t-90) REVERT: B 397 GLU cc_start: 0.8984 (pm20) cc_final: 0.8456 (tm-30) REVERT: B 587 MET cc_start: 0.8830 (mtm) cc_final: 0.8545 (mtp) REVERT: B 622 LEU cc_start: 0.9331 (tp) cc_final: 0.9130 (tp) REVERT: B 624 PHE cc_start: 0.9049 (m-80) cc_final: 0.8792 (m-80) REVERT: B 685 MET cc_start: 0.1805 (tpt) cc_final: 0.1510 (tpt) REVERT: B 761 MET cc_start: 0.8224 (mmp) cc_final: 0.8022 (mmp) REVERT: C 176 HIS cc_start: 0.9071 (t-90) cc_final: 0.8767 (t-90) REVERT: C 397 GLU cc_start: 0.8902 (pm20) cc_final: 0.8509 (tm-30) REVERT: C 624 PHE cc_start: 0.9028 (m-80) cc_final: 0.8816 (m-80) REVERT: C 685 MET cc_start: 0.1488 (tpt) cc_final: 0.1164 (tpt) REVERT: D 176 HIS cc_start: 0.9101 (t-90) cc_final: 0.8804 (t-90) REVERT: D 397 GLU cc_start: 0.8910 (pm20) cc_final: 0.8555 (tm-30) REVERT: D 587 MET cc_start: 0.8896 (mtm) cc_final: 0.8665 (mtp) REVERT: D 624 PHE cc_start: 0.9014 (m-80) cc_final: 0.8788 (m-80) REVERT: D 625 MET cc_start: 0.8867 (ptp) cc_final: 0.8495 (ptp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2469 time to fit residues: 89.6493 Evaluate side-chains 190 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.0040 chunk 212 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20136 Z= 0.125 Angle : 0.493 6.515 27288 Z= 0.263 Chirality : 0.035 0.150 3136 Planarity : 0.003 0.036 3408 Dihedral : 4.923 28.829 2692 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 54.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.33 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2424 helix: 0.83 (0.14), residues: 1396 sheet: -0.81 (0.58), residues: 76 loop : -3.78 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 586 HIS 0.003 0.001 HIS A 401 PHE 0.015 0.001 PHE D 624 TYR 0.013 0.001 TYR A 628 ARG 0.002 0.000 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9071 (t-90) cc_final: 0.8781 (t-90) REVERT: A 397 GLU cc_start: 0.8860 (pm20) cc_final: 0.8529 (tm-30) REVERT: A 482 MET cc_start: 0.8339 (mmm) cc_final: 0.7666 (mmt) REVERT: A 621 TYR cc_start: 0.9254 (t80) cc_final: 0.9052 (t80) REVERT: A 622 LEU cc_start: 0.9246 (tp) cc_final: 0.9034 (tp) REVERT: B 176 HIS cc_start: 0.9005 (t-90) cc_final: 0.8788 (t-90) REVERT: B 397 GLU cc_start: 0.8930 (pm20) cc_final: 0.8479 (tm-30) REVERT: B 587 MET cc_start: 0.8819 (mtm) cc_final: 0.8604 (mtp) REVERT: B 621 TYR cc_start: 0.9211 (t80) cc_final: 0.8936 (t80) REVERT: B 622 LEU cc_start: 0.9258 (tp) cc_final: 0.9053 (tp) REVERT: B 624 PHE cc_start: 0.9012 (m-80) cc_final: 0.8768 (m-80) REVERT: B 642 MET cc_start: 0.8674 (tpt) cc_final: 0.8454 (tpp) REVERT: B 685 MET cc_start: 0.1905 (tpt) cc_final: 0.1602 (tpt) REVERT: B 713 MET cc_start: 0.9271 (tpt) cc_final: 0.8876 (tpp) REVERT: B 761 MET cc_start: 0.8016 (mmp) cc_final: 0.7760 (mmp) REVERT: C 176 HIS cc_start: 0.9079 (t-90) cc_final: 0.8811 (t-90) REVERT: C 397 GLU cc_start: 0.8817 (pm20) cc_final: 0.8512 (tm-30) REVERT: C 482 MET cc_start: 0.8354 (mmm) cc_final: 0.7663 (mmt) REVERT: C 624 PHE cc_start: 0.8962 (m-80) cc_final: 0.8743 (m-80) REVERT: C 685 MET cc_start: 0.1508 (tpt) cc_final: 0.1268 (tpt) REVERT: D 176 HIS cc_start: 0.9074 (t-90) cc_final: 0.8815 (t-90) REVERT: D 397 GLU cc_start: 0.8839 (pm20) cc_final: 0.8605 (tm-30) REVERT: D 482 MET cc_start: 0.8209 (mmm) cc_final: 0.7751 (mmt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2835 time to fit residues: 107.0679 Evaluate side-chains 194 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20136 Z= 0.141 Angle : 0.495 6.142 27288 Z= 0.263 Chirality : 0.035 0.149 3136 Planarity : 0.003 0.047 3408 Dihedral : 4.759 27.754 2692 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 57.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.25 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2424 helix: 1.19 (0.14), residues: 1376 sheet: -0.69 (0.58), residues: 76 loop : -3.65 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 586 HIS 0.003 0.001 HIS C 447 PHE 0.023 0.001 PHE D 624 TYR 0.014 0.001 TYR A 628 ARG 0.002 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9075 (t-90) cc_final: 0.8797 (t-90) REVERT: A 397 GLU cc_start: 0.8822 (pm20) cc_final: 0.8526 (tm-30) REVERT: A 482 MET cc_start: 0.8360 (mmm) cc_final: 0.7675 (mmt) REVERT: A 622 LEU cc_start: 0.9228 (tp) cc_final: 0.8995 (tp) REVERT: B 176 HIS cc_start: 0.9002 (t-90) cc_final: 0.8802 (t-90) REVERT: B 397 GLU cc_start: 0.8873 (pm20) cc_final: 0.8457 (tm-30) REVERT: B 587 MET cc_start: 0.8802 (mtm) cc_final: 0.8595 (mtp) REVERT: B 621 TYR cc_start: 0.9216 (t80) cc_final: 0.8966 (t80) REVERT: B 622 LEU cc_start: 0.9244 (tp) cc_final: 0.9039 (tp) REVERT: B 624 PHE cc_start: 0.8997 (m-80) cc_final: 0.8782 (m-80) REVERT: B 685 MET cc_start: 0.1804 (tpt) cc_final: 0.1575 (tpt) REVERT: B 761 MET cc_start: 0.8010 (mmp) cc_final: 0.7773 (mmp) REVERT: C 176 HIS cc_start: 0.9082 (t-90) cc_final: 0.8824 (t-90) REVERT: C 397 GLU cc_start: 0.8765 (pm20) cc_final: 0.8518 (tm-30) REVERT: C 482 MET cc_start: 0.8388 (mmm) cc_final: 0.7681 (mmt) REVERT: C 622 LEU cc_start: 0.9174 (tp) cc_final: 0.8844 (tp) REVERT: C 685 MET cc_start: 0.1347 (tpt) cc_final: 0.1139 (tpt) REVERT: D 176 HIS cc_start: 0.9087 (t-90) cc_final: 0.8834 (t-90) REVERT: D 397 GLU cc_start: 0.8814 (pm20) cc_final: 0.8594 (tm-30) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2767 time to fit residues: 102.3427 Evaluate side-chains 193 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 116 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20136 Z= 0.186 Angle : 0.527 9.845 27288 Z= 0.278 Chirality : 0.035 0.140 3136 Planarity : 0.003 0.038 3408 Dihedral : 4.798 26.291 2692 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 61.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.20 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2424 helix: 1.13 (0.14), residues: 1396 sheet: -0.70 (0.59), residues: 76 loop : -3.63 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 586 HIS 0.004 0.001 HIS A 326 PHE 0.023 0.001 PHE A 624 TYR 0.014 0.001 TYR B 303 ARG 0.002 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9086 (t-90) cc_final: 0.8807 (t-90) REVERT: A 397 GLU cc_start: 0.8852 (pm20) cc_final: 0.8542 (tm-30) REVERT: A 482 MET cc_start: 0.8351 (mmm) cc_final: 0.7696 (mmt) REVERT: A 622 LEU cc_start: 0.9244 (tp) cc_final: 0.8979 (tp) REVERT: A 685 MET cc_start: 0.1617 (tpt) cc_final: 0.1412 (tpt) REVERT: B 176 HIS cc_start: 0.9025 (t-90) cc_final: 0.8809 (t-90) REVERT: B 397 GLU cc_start: 0.8875 (pm20) cc_final: 0.8479 (tm-30) REVERT: B 621 TYR cc_start: 0.9218 (t80) cc_final: 0.8986 (t80) REVERT: B 622 LEU cc_start: 0.9243 (tp) cc_final: 0.9037 (tp) REVERT: B 624 PHE cc_start: 0.9035 (m-80) cc_final: 0.8826 (m-80) REVERT: B 685 MET cc_start: 0.1875 (tpt) cc_final: 0.1673 (tpt) REVERT: B 761 MET cc_start: 0.8103 (mmp) cc_final: 0.7778 (mmp) REVERT: C 176 HIS cc_start: 0.9101 (t-90) cc_final: 0.8823 (t-90) REVERT: C 397 GLU cc_start: 0.8777 (pm20) cc_final: 0.8534 (tm-30) REVERT: C 482 MET cc_start: 0.8376 (mmm) cc_final: 0.7712 (mmt) REVERT: C 622 LEU cc_start: 0.9126 (tp) cc_final: 0.8797 (tp) REVERT: C 713 MET cc_start: 0.9162 (tpt) cc_final: 0.8943 (tpt) REVERT: D 176 HIS cc_start: 0.9116 (t-90) cc_final: 0.8858 (t-90) REVERT: D 397 GLU cc_start: 0.8806 (pm20) cc_final: 0.8583 (tm-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2760 time to fit residues: 99.5794 Evaluate side-chains 189 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 205 optimal weight: 0.0770 chunk 219 optimal weight: 6.9990 chunk 131 optimal weight: 0.0270 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.115 Angle : 0.470 6.902 27288 Z= 0.248 Chirality : 0.035 0.113 3136 Planarity : 0.003 0.034 3408 Dihedral : 4.507 24.858 2692 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 56.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.34 % Favored : 88.49 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2424 helix: 1.55 (0.14), residues: 1376 sheet: -0.59 (0.60), residues: 76 loop : -3.46 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 586 HIS 0.003 0.001 HIS C 447 PHE 0.027 0.001 PHE C 624 TYR 0.013 0.001 TYR A 628 ARG 0.002 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9077 (t-90) cc_final: 0.8817 (t-90) REVERT: A 397 GLU cc_start: 0.8765 (pm20) cc_final: 0.8558 (tm-30) REVERT: A 482 MET cc_start: 0.8344 (mmm) cc_final: 0.7685 (mmt) REVERT: A 605 MET cc_start: 0.9507 (ptt) cc_final: 0.8796 (ptt) REVERT: A 622 LEU cc_start: 0.9213 (tp) cc_final: 0.8966 (tp) REVERT: B 397 GLU cc_start: 0.8805 (pm20) cc_final: 0.8497 (tm-30) REVERT: B 556 TYR cc_start: 0.9118 (t80) cc_final: 0.8780 (t80) REVERT: B 587 MET cc_start: 0.8822 (mtm) cc_final: 0.8590 (mtp) REVERT: B 621 TYR cc_start: 0.9214 (t80) cc_final: 0.8989 (t80) REVERT: B 622 LEU cc_start: 0.9220 (tp) cc_final: 0.9016 (tp) REVERT: B 710 LEU cc_start: 0.9838 (mm) cc_final: 0.9627 (mp) REVERT: B 761 MET cc_start: 0.7946 (mmp) cc_final: 0.7736 (mmp) REVERT: C 176 HIS cc_start: 0.9081 (t-90) cc_final: 0.8832 (t-90) REVERT: C 482 MET cc_start: 0.8409 (mmm) cc_final: 0.7736 (mmt) REVERT: C 622 LEU cc_start: 0.9154 (tp) cc_final: 0.8817 (tp) REVERT: D 176 HIS cc_start: 0.9083 (t-90) cc_final: 0.8863 (t-90) REVERT: D 556 TYR cc_start: 0.9208 (t80) cc_final: 0.9001 (t80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2780 time to fit residues: 104.8995 Evaluate side-chains 193 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 141 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 223 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 20 optimal weight: 0.0370 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20136 Z= 0.158 Angle : 0.499 9.151 27288 Z= 0.262 Chirality : 0.035 0.131 3136 Planarity : 0.003 0.036 3408 Dihedral : 4.507 24.182 2692 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 59.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.50 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2424 helix: 1.55 (0.14), residues: 1376 sheet: -0.41 (0.62), residues: 76 loop : -3.42 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 586 HIS 0.003 0.001 HIS A 265 PHE 0.021 0.001 PHE A 707 TYR 0.014 0.001 TYR B 628 ARG 0.002 0.000 ARG D 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9066 (t-90) cc_final: 0.8813 (t-90) REVERT: A 397 GLU cc_start: 0.8742 (pm20) cc_final: 0.8540 (tm-30) REVERT: A 482 MET cc_start: 0.8330 (mmm) cc_final: 0.7712 (mmt) REVERT: A 622 LEU cc_start: 0.9201 (tp) cc_final: 0.8942 (tp) REVERT: B 176 HIS cc_start: 0.9058 (t-90) cc_final: 0.8770 (t-170) REVERT: B 397 GLU cc_start: 0.8812 (pm20) cc_final: 0.8503 (tm-30) REVERT: B 622 LEU cc_start: 0.9213 (tp) cc_final: 0.8974 (tp) REVERT: B 761 MET cc_start: 0.8044 (mmp) cc_final: 0.7820 (mmp) REVERT: C 176 HIS cc_start: 0.9099 (t-90) cc_final: 0.8834 (t-90) REVERT: C 482 MET cc_start: 0.8430 (mmm) cc_final: 0.7739 (mmt) REVERT: C 622 LEU cc_start: 0.9120 (tp) cc_final: 0.8807 (tp) REVERT: D 176 HIS cc_start: 0.9100 (t-90) cc_final: 0.8881 (t-90) REVERT: D 556 TYR cc_start: 0.9201 (t80) cc_final: 0.8977 (t80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2781 time to fit residues: 102.4596 Evaluate side-chains 190 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.0030 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 199 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.097995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074670 restraints weight = 90911.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076671 restraints weight = 54126.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077963 restraints weight = 38807.536| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20136 Z= 0.113 Angle : 0.469 8.203 27288 Z= 0.247 Chirality : 0.035 0.141 3136 Planarity : 0.003 0.035 3408 Dihedral : 4.375 23.451 2692 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 56.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.14 % Favored : 88.70 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2424 helix: 1.73 (0.14), residues: 1380 sheet: -0.24 (0.63), residues: 76 loop : -3.23 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 586 HIS 0.003 0.001 HIS C 447 PHE 0.038 0.001 PHE C 707 TYR 0.012 0.001 TYR A 628 ARG 0.005 0.000 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.63 seconds wall clock time: 71 minutes 4.31 seconds (4264.31 seconds total)