Starting phenix.real_space_refine on Sun Apr 7 09:31:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl2_32574/04_2024/7wl2_32574.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 5.68, per 1000 atoms: 0.56 Number of scatterers: 10198 At special positions: 0 Unit cell: (86.818, 128.658, 116.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 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 - 3.50 Amino acid : False - 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 66.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.725A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.875A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.928A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.005A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.877A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.675A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.865A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 216 through 240 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.505A pdb=" N TYR A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.514A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.807A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.568A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.800A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.588A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.646A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.865A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.670A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.852A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.570A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.515A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.722A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.652A pdb=" N VAL B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.932A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 106 removed outlier: 3.809A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 removed outlier: 3.578A pdb=" N ALA B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.893A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.557A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 4.062A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.789A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.529A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.658A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 375 removed outlier: 3.719A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.613A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.798A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.503A pdb=" N ALA B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.785A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.685A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.693A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 removed outlier: 3.501A pdb=" N LYS B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.787A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.571A pdb=" N VAL B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.041A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.573A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.503A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.781A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 removed outlier: 4.128A pdb=" N VAL A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 175 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.510A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164 removed outlier: 4.191A pdb=" N VAL B 163 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR B 175 " --> pdb=" O VAL B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.508A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1671 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: 3.04 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3214 1.34 - 1.46: 2202 1.46 - 1.58: 4920 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA VAL A 163 " pdb=" CB VAL A 163 " ideal model delta sigma weight residual 1.540 1.527 0.013 7.70e-03 1.69e+04 2.75e+00 bond pdb=" CA VAL B 163 " pdb=" CB VAL B 163 " ideal model delta sigma weight residual 1.541 1.526 0.015 1.24e-02 6.50e+03 1.44e+00 bond pdb=" C VAL A 163 " pdb=" O VAL A 163 " ideal model delta sigma weight residual 1.232 1.242 -0.009 8.90e-03 1.26e+04 1.12e+00 bond pdb=" CA THR A 45 " pdb=" CB THR A 45 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.92e-01 bond pdb=" CA THR B 45 " pdb=" CB THR B 45 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.79e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 299 107.43 - 114.08: 6177 114.08 - 120.72: 4403 120.72 - 127.36: 3185 127.36 - 134.01: 72 Bond angle restraints: 14136 Sorted by residual: angle pdb=" N PHE B 128 " pdb=" CA PHE B 128 " pdb=" C PHE B 128 " ideal model delta sigma weight residual 114.56 109.13 5.43 1.27e+00 6.20e-01 1.83e+01 angle pdb=" N VAL A 699 " pdb=" CA VAL A 699 " pdb=" C VAL A 699 " ideal model delta sigma weight residual 111.81 108.76 3.05 8.60e-01 1.35e+00 1.26e+01 angle pdb=" N VAL B 699 " pdb=" CA VAL B 699 " pdb=" C VAL B 699 " ideal model delta sigma weight residual 111.81 109.10 2.71 8.60e-01 1.35e+00 9.89e+00 angle pdb=" N ILE B 686 " pdb=" CA ILE B 686 " pdb=" C ILE B 686 " ideal model delta sigma weight residual 111.77 109.05 2.72 1.04e+00 9.25e-01 6.84e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.68 -4.71 1.80e+00 3.09e-01 6.83e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 5961 16.59 - 33.18: 182 33.18 - 49.77: 28 49.77 - 66.36: 8 66.36 - 82.95: 3 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" N MET B 488 " pdb=" CA MET B 488 " pdb=" CB MET B 488 " pdb=" CG MET B 488 " ideal model delta sinusoidal sigma weight residual -180.00 -121.83 -58.17 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -122.73 -57.27 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 998 0.026 - 0.051: 405 0.051 - 0.077: 217 0.077 - 0.102: 79 0.102 - 0.128: 19 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 300 " pdb=" N ILE B 300 " pdb=" C ILE B 300 " pdb=" CB ILE B 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE A 300 " pdb=" N ILE A 300 " pdb=" C ILE A 300 " pdb=" CB ILE A 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 553 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 553 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 112 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.018 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1140 2.75 - 3.28: 10835 3.28 - 3.82: 16534 3.82 - 4.36: 19706 4.36 - 4.90: 33830 Nonbonded interactions: 82045 Sorted by model distance: nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.207 2.440 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.231 2.440 nonbonded pdb=" O TYR A 247 " pdb=" OG SER A 252 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR B 118 " pdb=" O GLY B 334 " model vdw 2.277 2.440 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.282 2.520 ... (remaining 82040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 6.870 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 29.880 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.002 0.021 10400 Z= 0.119 Angle : 0.490 5.616 14136 Z= 0.302 Chirality : 0.037 0.128 1718 Planarity : 0.003 0.036 1758 Dihedral : 8.514 82.947 3710 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 2.14 % Allowed : 5.61 % Favored : 92.25 % 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: -4.09 (0.19), residues: 1322 helix: -2.28 (0.14), residues: 854 sheet: -3.88 (0.57), residues: 36 loop : -3.19 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 83 HIS 0.002 0.000 HIS B 656 PHE 0.009 0.001 PHE B 555 TYR 0.007 0.001 TYR A 377 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 385 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5719 (p0) REVERT: A 237 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8078 (ttpt) REVERT: A 254 ILE cc_start: 0.7961 (mm) cc_final: 0.7704 (mm) REVERT: A 369 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7445 (mmtp) REVERT: A 377 TYR cc_start: 0.7118 (p90) cc_final: 0.6908 (p90) REVERT: A 384 GLU cc_start: 0.7180 (tp30) cc_final: 0.6581 (tp30) REVERT: A 385 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7054 (t80) REVERT: A 405 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 414 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6342 (tm-30) REVERT: A 447 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7921 (ttmt) REVERT: A 448 SER cc_start: 0.8224 (p) cc_final: 0.7961 (p) REVERT: A 459 LYS cc_start: 0.7769 (tppp) cc_final: 0.7016 (tppp) REVERT: A 528 ASP cc_start: 0.8241 (p0) cc_final: 0.8040 (p0) REVERT: A 531 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8050 (mmtt) REVERT: A 580 LYS cc_start: 0.6322 (ttpt) cc_final: 0.5758 (tmtt) REVERT: A 652 LYS cc_start: 0.5141 (pttt) cc_final: 0.4156 (pttt) REVERT: A 684 GLN cc_start: 0.8051 (tp40) cc_final: 0.7549 (tp-100) REVERT: A 687 ASP cc_start: 0.7271 (t70) cc_final: 0.6981 (t0) REVERT: A 717 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7943 (mtt90) REVERT: B 87 ASP cc_start: 0.6927 (m-30) cc_final: 0.6609 (m-30) REVERT: B 92 VAL cc_start: 0.8334 (m) cc_final: 0.8079 (t) REVERT: B 245 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7657 (ttmt) REVERT: B 255 TYR cc_start: 0.8269 (m-10) cc_final: 0.7878 (m-10) REVERT: B 289 ASN cc_start: 0.7756 (t0) cc_final: 0.7351 (t0) REVERT: B 303 GLU cc_start: 0.6944 (mp0) cc_final: 0.6667 (mp0) REVERT: B 384 GLU cc_start: 0.7820 (tp30) cc_final: 0.7546 (tp30) REVERT: B 385 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8097 (m-80) REVERT: B 447 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7846 (mtmm) REVERT: B 475 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7442 (t0) REVERT: B 478 ASP cc_start: 0.7298 (m-30) cc_final: 0.6603 (m-30) REVERT: B 492 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (pp) REVERT: B 499 LEU cc_start: 0.8440 (tp) cc_final: 0.8175 (tp) REVERT: B 531 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7879 (mmtm) REVERT: B 538 ASN cc_start: 0.6687 (p0) cc_final: 0.6347 (p0) REVERT: B 563 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7969 (mmmt) REVERT: B 564 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7783 (ttmm) REVERT: B 580 LYS cc_start: 0.6744 (ttpt) cc_final: 0.6296 (tmtt) REVERT: B 669 ASP cc_start: 0.6822 (t0) cc_final: 0.6578 (t0) REVERT: B 681 LYS cc_start: 0.8007 (mptt) cc_final: 0.7654 (mptt) REVERT: B 682 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6861 (mm-30) REVERT: B 685 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7436 (mtm180) REVERT: B 687 ASP cc_start: 0.7193 (t70) cc_final: 0.6988 (t0) REVERT: B 714 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: B 732 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6718 (tm-30) outliers start: 24 outliers final: 4 residues processed: 398 average time/residue: 0.2864 time to fit residues: 148.5770 Evaluate side-chains 325 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 315 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 673 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 135 HIS A 207 GLN A 262 GLN A 413 GLN A 475 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 101 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 413 GLN B 464 GLN B 475 ASN ** B 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 HIS ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10400 Z= 0.252 Angle : 0.582 10.893 14136 Z= 0.302 Chirality : 0.043 0.207 1718 Planarity : 0.005 0.050 1758 Dihedral : 4.832 54.439 1432 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.21 % Allowed : 15.69 % Favored : 81.11 % 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: -2.00 (0.22), residues: 1322 helix: -0.52 (0.17), residues: 872 sheet: -3.30 (0.66), residues: 36 loop : -2.76 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.011 0.001 HIS A 656 PHE 0.027 0.002 PHE B 130 TYR 0.022 0.002 TYR B 377 ARG 0.007 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 326 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6885 (mtt-85) cc_final: 0.6643 (mmm160) REVERT: A 182 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.6028 (p0) REVERT: A 247 TYR cc_start: 0.7897 (m-10) cc_final: 0.6919 (m-80) REVERT: A 287 GLU cc_start: 0.7129 (pp20) cc_final: 0.6767 (pp20) REVERT: A 289 ASN cc_start: 0.7879 (t0) cc_final: 0.7632 (t0) REVERT: A 318 ASN cc_start: 0.7571 (t0) cc_final: 0.7365 (t0) REVERT: A 320 GLU cc_start: 0.6442 (tp30) cc_final: 0.6233 (tp30) REVERT: A 361 TYR cc_start: 0.8184 (t80) cc_final: 0.7682 (t80) REVERT: A 371 TYR cc_start: 0.7991 (m-80) cc_final: 0.7705 (m-80) REVERT: A 377 TYR cc_start: 0.7619 (p90) cc_final: 0.7340 (p90) REVERT: A 384 GLU cc_start: 0.7318 (tp30) cc_final: 0.6696 (tp30) REVERT: A 385 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 432 MET cc_start: 0.7655 (tpt) cc_final: 0.7046 (tpt) REVERT: A 448 SER cc_start: 0.8154 (p) cc_final: 0.7917 (p) REVERT: A 459 LYS cc_start: 0.7529 (tppp) cc_final: 0.7248 (tppp) REVERT: A 475 ASN cc_start: 0.7860 (t0) cc_final: 0.7428 (t0) REVERT: A 478 ASP cc_start: 0.7047 (m-30) cc_final: 0.6564 (m-30) REVERT: A 503 LEU cc_start: 0.8057 (mt) cc_final: 0.7831 (mm) REVERT: A 518 TRP cc_start: 0.8597 (p-90) cc_final: 0.8338 (p-90) REVERT: A 580 LYS cc_start: 0.6571 (ttpt) cc_final: 0.6159 (ttpt) REVERT: A 652 LYS cc_start: 0.5177 (pttt) cc_final: 0.4075 (pttt) REVERT: A 684 GLN cc_start: 0.7973 (tp40) cc_final: 0.7688 (tp-100) REVERT: A 687 ASP cc_start: 0.7304 (t70) cc_final: 0.6992 (t0) REVERT: B 39 ARG cc_start: 0.7796 (tpp80) cc_final: 0.7588 (tpp-160) REVERT: B 87 ASP cc_start: 0.6979 (m-30) cc_final: 0.6743 (m-30) REVERT: B 101 GLN cc_start: 0.8220 (mt0) cc_final: 0.8003 (mt0) REVERT: B 137 SER cc_start: 0.8210 (p) cc_final: 0.7970 (t) REVERT: B 245 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7654 (ttmt) REVERT: B 255 TYR cc_start: 0.8372 (m-10) cc_final: 0.7606 (m-10) REVERT: B 289 ASN cc_start: 0.8023 (t0) cc_final: 0.7648 (t0) REVERT: B 309 ILE cc_start: 0.8458 (tt) cc_final: 0.8228 (pt) REVERT: B 318 ASN cc_start: 0.7462 (t0) cc_final: 0.7191 (t0) REVERT: B 320 GLU cc_start: 0.6697 (tp30) cc_final: 0.6479 (tp30) REVERT: B 370 VAL cc_start: 0.8437 (t) cc_final: 0.8217 (t) REVERT: B 384 GLU cc_start: 0.7661 (tp30) cc_final: 0.7348 (tp30) REVERT: B 385 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: B 459 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7382 (tppp) REVERT: B 462 PHE cc_start: 0.8094 (m-10) cc_final: 0.7829 (m-10) REVERT: B 475 ASN cc_start: 0.7860 (t0) cc_final: 0.7574 (t0) REVERT: B 492 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8131 (pt) REVERT: B 538 ASN cc_start: 0.6875 (p0) cc_final: 0.6517 (p0) REVERT: B 560 ASP cc_start: 0.7302 (m-30) cc_final: 0.7027 (m-30) REVERT: B 580 LYS cc_start: 0.6856 (ttpt) cc_final: 0.6508 (ttpt) REVERT: B 681 LYS cc_start: 0.8090 (mptt) cc_final: 0.7774 (mptt) REVERT: B 682 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 687 ASP cc_start: 0.7249 (t70) cc_final: 0.7020 (t0) REVERT: B 731 ASN cc_start: 0.7173 (m110) cc_final: 0.6911 (m110) outliers start: 36 outliers final: 21 residues processed: 341 average time/residue: 0.2786 time to fit residues: 124.5746 Evaluate side-chains 321 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 295 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10400 Z= 0.197 Angle : 0.537 9.637 14136 Z= 0.279 Chirality : 0.041 0.147 1718 Planarity : 0.004 0.045 1758 Dihedral : 4.660 56.309 1426 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 4.19 % Allowed : 17.38 % Favored : 78.43 % 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 (0.23), residues: 1322 helix: 0.30 (0.18), residues: 854 sheet: -2.87 (0.68), residues: 36 loop : -2.38 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS B 160 PHE 0.016 0.001 PHE B 130 TYR 0.023 0.001 TYR B 377 ARG 0.008 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 300 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8031 (p) REVERT: A 79 ARG cc_start: 0.6833 (mtt-85) cc_final: 0.6593 (mmm160) REVERT: A 182 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.6026 (p0) REVERT: A 286 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7943 (ttmm) REVERT: A 287 GLU cc_start: 0.7129 (pp20) cc_final: 0.6784 (pp20) REVERT: A 329 LYS cc_start: 0.8110 (pttt) cc_final: 0.7788 (ptmm) REVERT: A 370 VAL cc_start: 0.8319 (t) cc_final: 0.8075 (t) REVERT: A 371 TYR cc_start: 0.8008 (m-80) cc_final: 0.7789 (m-80) REVERT: A 377 TYR cc_start: 0.7694 (p90) cc_final: 0.7434 (p90) REVERT: A 384 GLU cc_start: 0.7322 (tp30) cc_final: 0.6697 (tp30) REVERT: A 385 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7093 (t80) REVERT: A 448 SER cc_start: 0.8134 (p) cc_final: 0.7863 (p) REVERT: A 475 ASN cc_start: 0.7708 (t0) cc_final: 0.7264 (t0) REVERT: A 478 ASP cc_start: 0.7162 (m-30) cc_final: 0.6649 (m-30) REVERT: A 518 TRP cc_start: 0.8501 (p-90) cc_final: 0.8249 (p-90) REVERT: A 576 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7249 (ttm-80) REVERT: A 681 LYS cc_start: 0.7615 (mptt) cc_final: 0.7330 (mmtp) REVERT: A 684 GLN cc_start: 0.8028 (tp40) cc_final: 0.7695 (tp-100) REVERT: A 687 ASP cc_start: 0.7306 (t70) cc_final: 0.6960 (t0) REVERT: A 730 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: B 21 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 87 ASP cc_start: 0.7058 (m-30) cc_final: 0.6561 (m-30) REVERT: B 245 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7633 (ttmt) REVERT: B 255 TYR cc_start: 0.8401 (m-10) cc_final: 0.7581 (m-10) REVERT: B 289 ASN cc_start: 0.8059 (t0) cc_final: 0.7668 (t0) REVERT: B 303 GLU cc_start: 0.6848 (mp0) cc_final: 0.6602 (mp0) REVERT: B 318 ASN cc_start: 0.7508 (t0) cc_final: 0.7238 (t0) REVERT: B 320 GLU cc_start: 0.6733 (tp30) cc_final: 0.6500 (tp30) REVERT: B 370 VAL cc_start: 0.8424 (t) cc_final: 0.8197 (t) REVERT: B 384 GLU cc_start: 0.7602 (tp30) cc_final: 0.7290 (tp30) REVERT: B 385 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 414 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 459 LYS cc_start: 0.7670 (tppp) cc_final: 0.7391 (tppp) REVERT: B 462 PHE cc_start: 0.8143 (m-10) cc_final: 0.7814 (m-10) REVERT: B 475 ASN cc_start: 0.7821 (t0) cc_final: 0.7481 (t0) REVERT: B 492 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 538 ASN cc_start: 0.6937 (p0) cc_final: 0.6569 (p0) REVERT: B 560 ASP cc_start: 0.7345 (m-30) cc_final: 0.7040 (m-30) REVERT: B 681 LYS cc_start: 0.7965 (mptt) cc_final: 0.7668 (mptt) REVERT: B 682 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6710 (mm-30) REVERT: B 687 ASP cc_start: 0.7267 (t70) cc_final: 0.6937 (t70) outliers start: 47 outliers final: 31 residues processed: 327 average time/residue: 0.2688 time to fit residues: 116.0311 Evaluate side-chains 331 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 292 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0970 chunk 90 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 241 ASN B 579 ASN B 696 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10400 Z= 0.192 Angle : 0.534 8.130 14136 Z= 0.278 Chirality : 0.041 0.140 1718 Planarity : 0.004 0.044 1758 Dihedral : 4.675 53.547 1426 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.43 % Favored : 93.42 % Rotamer: Outliers : 4.81 % Allowed : 18.00 % Favored : 77.18 % 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: -0.50 (0.24), residues: 1322 helix: 0.65 (0.18), residues: 858 sheet: -2.48 (0.72), residues: 36 loop : -2.14 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS A 656 PHE 0.012 0.001 PHE A 115 TYR 0.019 0.001 TYR B 377 ARG 0.006 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 301 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8070 (p) REVERT: A 79 ARG cc_start: 0.6827 (mtt-85) cc_final: 0.6591 (mmm160) REVERT: A 182 ASP cc_start: 0.6409 (OUTLIER) cc_final: 0.6067 (p0) REVERT: A 248 ASN cc_start: 0.7703 (m-40) cc_final: 0.7469 (m-40) REVERT: A 286 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7942 (ttmm) REVERT: A 287 GLU cc_start: 0.7103 (pp20) cc_final: 0.6725 (pp20) REVERT: A 329 LYS cc_start: 0.8079 (pttt) cc_final: 0.7763 (ptmm) REVERT: A 361 TYR cc_start: 0.8066 (t80) cc_final: 0.7866 (t80) REVERT: A 370 VAL cc_start: 0.8368 (t) cc_final: 0.8138 (t) REVERT: A 377 TYR cc_start: 0.7453 (p90) cc_final: 0.7241 (p90) REVERT: A 384 GLU cc_start: 0.7329 (tp30) cc_final: 0.6688 (tp30) REVERT: A 385 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7127 (t80) REVERT: A 475 ASN cc_start: 0.7674 (t0) cc_final: 0.7325 (t0) REVERT: A 478 ASP cc_start: 0.7201 (m-30) cc_final: 0.6779 (m-30) REVERT: A 576 ARG cc_start: 0.7491 (mtt90) cc_final: 0.7255 (ttm-80) REVERT: A 684 GLN cc_start: 0.8018 (tp40) cc_final: 0.7695 (tp-100) REVERT: A 687 ASP cc_start: 0.7314 (t70) cc_final: 0.6957 (t0) REVERT: A 730 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: B 21 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8085 (p) REVERT: B 255 TYR cc_start: 0.8387 (m-10) cc_final: 0.7540 (m-80) REVERT: B 289 ASN cc_start: 0.8016 (t0) cc_final: 0.7635 (t0) REVERT: B 303 GLU cc_start: 0.6810 (mp0) cc_final: 0.6601 (mp0) REVERT: B 318 ASN cc_start: 0.7546 (t0) cc_final: 0.7156 (t0) REVERT: B 370 VAL cc_start: 0.8420 (t) cc_final: 0.8192 (t) REVERT: B 384 GLU cc_start: 0.7559 (tp30) cc_final: 0.7250 (tp30) REVERT: B 385 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: B 414 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6673 (tm-30) REVERT: B 459 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7388 (tppp) REVERT: B 462 PHE cc_start: 0.8133 (m-10) cc_final: 0.7805 (m-10) REVERT: B 475 ASN cc_start: 0.7782 (t0) cc_final: 0.7439 (t0) REVERT: B 492 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8215 (pt) REVERT: B 519 ASN cc_start: 0.8230 (m110) cc_final: 0.7996 (m-40) REVERT: B 538 ASN cc_start: 0.6982 (p0) cc_final: 0.6616 (p0) REVERT: B 560 ASP cc_start: 0.7338 (m-30) cc_final: 0.7012 (m-30) REVERT: B 580 LYS cc_start: 0.6819 (ttpt) cc_final: 0.6444 (tmtt) REVERT: B 681 LYS cc_start: 0.7939 (mptt) cc_final: 0.7640 (mptt) REVERT: B 682 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 687 ASP cc_start: 0.7256 (t70) cc_final: 0.6907 (t70) REVERT: B 696 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6185 (mm-40) REVERT: B 731 ASN cc_start: 0.7250 (m110) cc_final: 0.6961 (m110) outliers start: 54 outliers final: 36 residues processed: 331 average time/residue: 0.2774 time to fit residues: 121.0275 Evaluate side-chains 331 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 285 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 696 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 457 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10400 Z= 0.261 Angle : 0.564 8.195 14136 Z= 0.296 Chirality : 0.043 0.164 1718 Planarity : 0.004 0.048 1758 Dihedral : 4.845 56.780 1426 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 5.70 % Allowed : 17.29 % Favored : 77.01 % 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: -0.29 (0.24), residues: 1322 helix: 0.75 (0.18), residues: 858 sheet: -1.71 (0.80), residues: 36 loop : -1.95 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 PHE 0.013 0.001 PHE A 115 TYR 0.024 0.002 TYR B 377 ARG 0.010 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 306 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8136 (p) REVERT: A 182 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6172 (p0) REVERT: A 286 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7950 (ttmm) REVERT: A 287 GLU cc_start: 0.7162 (pp20) cc_final: 0.6783 (pp20) REVERT: A 329 LYS cc_start: 0.8108 (pttt) cc_final: 0.7789 (ptmm) REVERT: A 361 TYR cc_start: 0.8054 (t80) cc_final: 0.7799 (t80) REVERT: A 370 VAL cc_start: 0.8398 (t) cc_final: 0.8114 (t) REVERT: A 384 GLU cc_start: 0.7438 (tp30) cc_final: 0.6796 (tp30) REVERT: A 385 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 576 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7258 (ttm-80) REVERT: A 684 GLN cc_start: 0.8013 (tp40) cc_final: 0.7746 (tp40) REVERT: A 687 ASP cc_start: 0.7313 (t70) cc_final: 0.6953 (t0) REVERT: A 730 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: B 21 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8110 (p) REVERT: B 79 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6971 (ttm170) REVERT: B 105 TYR cc_start: 0.8354 (m-10) cc_final: 0.8086 (m-80) REVERT: B 118 TYR cc_start: 0.8062 (m-10) cc_final: 0.7784 (m-10) REVERT: B 138 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8437 (p) REVERT: B 255 TYR cc_start: 0.8394 (m-10) cc_final: 0.7546 (m-80) REVERT: B 289 ASN cc_start: 0.8081 (t0) cc_final: 0.7692 (t0) REVERT: B 318 ASN cc_start: 0.7598 (t0) cc_final: 0.7309 (t0) REVERT: B 370 VAL cc_start: 0.8424 (t) cc_final: 0.8189 (t) REVERT: B 378 VAL cc_start: 0.8368 (t) cc_final: 0.7953 (p) REVERT: B 385 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7815 (m-80) REVERT: B 414 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6665 (tm-30) REVERT: B 459 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7394 (tppp) REVERT: B 462 PHE cc_start: 0.8163 (m-10) cc_final: 0.7789 (m-80) REVERT: B 475 ASN cc_start: 0.7718 (t0) cc_final: 0.7425 (t0) REVERT: B 492 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (pt) REVERT: B 519 ASN cc_start: 0.8218 (m110) cc_final: 0.7999 (m-40) REVERT: B 538 ASN cc_start: 0.7103 (p0) cc_final: 0.6732 (p0) REVERT: B 560 ASP cc_start: 0.7358 (m-30) cc_final: 0.7048 (m-30) REVERT: B 681 LYS cc_start: 0.7907 (mptt) cc_final: 0.7627 (mptt) REVERT: B 687 ASP cc_start: 0.7221 (t70) cc_final: 0.6889 (t70) REVERT: B 691 TYR cc_start: 0.7948 (m-80) cc_final: 0.7716 (m-80) outliers start: 64 outliers final: 43 residues processed: 343 average time/residue: 0.2713 time to fit residues: 123.0599 Evaluate side-chains 356 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 303 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B 241 ASN B 375 HIS B 457 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10400 Z= 0.208 Angle : 0.556 7.495 14136 Z= 0.292 Chirality : 0.042 0.169 1718 Planarity : 0.004 0.045 1758 Dihedral : 4.867 57.384 1426 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 5.35 % Allowed : 18.09 % Favored : 76.56 % 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: -0.08 (0.24), residues: 1322 helix: 0.89 (0.18), residues: 858 sheet: -1.18 (0.86), residues: 36 loop : -1.87 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS B 160 PHE 0.019 0.001 PHE A 130 TYR 0.026 0.001 TYR B 377 ARG 0.008 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 313 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 182 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6145 (p0) REVERT: A 247 TYR cc_start: 0.7826 (m-10) cc_final: 0.6838 (m-80) REVERT: A 248 ASN cc_start: 0.7723 (m-40) cc_final: 0.7514 (m-40) REVERT: A 287 GLU cc_start: 0.7153 (pp20) cc_final: 0.6741 (pp20) REVERT: A 361 TYR cc_start: 0.8099 (t80) cc_final: 0.7887 (t80) REVERT: A 370 VAL cc_start: 0.8402 (t) cc_final: 0.8131 (t) REVERT: A 384 GLU cc_start: 0.7417 (tp30) cc_final: 0.6786 (tp30) REVERT: A 385 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7180 (t80) REVERT: A 576 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7252 (ttm-80) REVERT: A 580 LYS cc_start: 0.6589 (ttpt) cc_final: 0.6167 (ttpt) REVERT: A 684 GLN cc_start: 0.8008 (tp40) cc_final: 0.7729 (tp40) REVERT: A 687 ASP cc_start: 0.7333 (t70) cc_final: 0.6954 (t0) REVERT: A 730 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: B 21 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 79 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6923 (ttm170) REVERT: B 105 TYR cc_start: 0.8356 (m-10) cc_final: 0.8071 (m-80) REVERT: B 118 TYR cc_start: 0.8043 (m-10) cc_final: 0.7762 (m-10) REVERT: B 255 TYR cc_start: 0.8380 (m-10) cc_final: 0.7568 (m-10) REVERT: B 289 ASN cc_start: 0.8062 (t0) cc_final: 0.7668 (t0) REVERT: B 370 VAL cc_start: 0.8421 (t) cc_final: 0.8193 (t) REVERT: B 385 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: B 414 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6638 (tm-30) REVERT: B 459 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7379 (tppp) REVERT: B 492 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (pt) REVERT: B 531 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7803 (mmmm) REVERT: B 538 ASN cc_start: 0.7119 (p0) cc_final: 0.6751 (p0) REVERT: B 560 ASP cc_start: 0.7351 (m-30) cc_final: 0.7041 (m-30) REVERT: B 681 LYS cc_start: 0.7872 (mptt) cc_final: 0.7613 (mptt) REVERT: B 682 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6385 (mm-30) REVERT: B 687 ASP cc_start: 0.7212 (t70) cc_final: 0.6889 (t70) outliers start: 60 outliers final: 43 residues processed: 342 average time/residue: 0.2745 time to fit residues: 123.0531 Evaluate side-chains 355 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 304 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 58 optimal weight: 0.0060 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 579 ASN ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN B 241 ASN B 375 HIS B 457 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10400 Z= 0.185 Angle : 0.553 6.520 14136 Z= 0.291 Chirality : 0.041 0.152 1718 Planarity : 0.004 0.052 1758 Dihedral : 4.853 57.015 1426 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 5.26 % Allowed : 19.16 % Favored : 75.58 % 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: 0.07 (0.24), residues: 1322 helix: 0.99 (0.18), residues: 860 sheet: -0.93 (0.89), residues: 36 loop : -1.81 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS B 723 PHE 0.016 0.001 PHE A 130 TYR 0.025 0.001 TYR B 377 ARG 0.013 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 313 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8157 (p) REVERT: A 66 LYS cc_start: 0.8122 (tptp) cc_final: 0.7632 (tptp) REVERT: A 182 ASP cc_start: 0.6459 (OUTLIER) cc_final: 0.6131 (p0) REVERT: A 247 TYR cc_start: 0.7821 (m-10) cc_final: 0.6749 (m-80) REVERT: A 248 ASN cc_start: 0.7730 (m-40) cc_final: 0.7519 (m-40) REVERT: A 287 GLU cc_start: 0.7129 (pp20) cc_final: 0.6723 (pp20) REVERT: A 370 VAL cc_start: 0.8412 (t) cc_final: 0.8124 (t) REVERT: A 384 GLU cc_start: 0.7406 (tp30) cc_final: 0.6760 (tp30) REVERT: A 385 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 475 ASN cc_start: 0.7741 (t0) cc_final: 0.7512 (t0) REVERT: A 492 LEU cc_start: 0.8654 (pt) cc_final: 0.8453 (pt) REVERT: A 531 LYS cc_start: 0.8166 (mmtp) cc_final: 0.7955 (mmtt) REVERT: A 576 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7236 (ttm-80) REVERT: A 580 LYS cc_start: 0.6621 (ttpt) cc_final: 0.6183 (ttpt) REVERT: A 684 GLN cc_start: 0.8002 (tp40) cc_final: 0.7729 (tp40) REVERT: A 687 ASP cc_start: 0.7323 (t70) cc_final: 0.6947 (t0) REVERT: A 730 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: B 21 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (p) REVERT: B 39 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7328 (mtm-85) REVERT: B 77 LYS cc_start: 0.8258 (ttmm) cc_final: 0.8051 (ttmm) REVERT: B 79 ARG cc_start: 0.7353 (ttm170) cc_final: 0.6968 (ttm170) REVERT: B 105 TYR cc_start: 0.8354 (m-10) cc_final: 0.8109 (m-80) REVERT: B 118 TYR cc_start: 0.8032 (m-10) cc_final: 0.7751 (m-10) REVERT: B 255 TYR cc_start: 0.8380 (m-10) cc_final: 0.7559 (m-10) REVERT: B 289 ASN cc_start: 0.8009 (t0) cc_final: 0.7594 (t0) REVERT: B 370 VAL cc_start: 0.8403 (t) cc_final: 0.8180 (t) REVERT: B 385 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: B 414 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 459 LYS cc_start: 0.7690 (tppp) cc_final: 0.7374 (tppp) REVERT: B 492 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8278 (pt) REVERT: B 538 ASN cc_start: 0.7108 (p0) cc_final: 0.6744 (p0) REVERT: B 560 ASP cc_start: 0.7350 (m-30) cc_final: 0.7050 (m-30) REVERT: B 681 LYS cc_start: 0.7887 (mptt) cc_final: 0.7644 (mptt) REVERT: B 682 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6271 (mm-30) REVERT: B 687 ASP cc_start: 0.7210 (t70) cc_final: 0.6907 (t70) outliers start: 59 outliers final: 39 residues processed: 344 average time/residue: 0.2766 time to fit residues: 125.9557 Evaluate side-chains 352 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 306 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10400 Z= 0.267 Angle : 0.588 6.555 14136 Z= 0.312 Chirality : 0.043 0.152 1718 Planarity : 0.004 0.053 1758 Dihedral : 4.926 52.462 1426 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 5.44 % Allowed : 19.07 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1322 helix: 0.97 (0.18), residues: 858 sheet: -0.99 (0.86), residues: 36 loop : -1.83 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.003 0.001 HIS A 723 PHE 0.014 0.001 PHE A 130 TYR 0.023 0.002 TYR A 377 ARG 0.011 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 316 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 66 LYS cc_start: 0.8122 (tptp) cc_final: 0.7646 (tptp) REVERT: A 127 TYR cc_start: 0.8245 (t80) cc_final: 0.8017 (t80) REVERT: A 182 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6198 (p0) REVERT: A 247 TYR cc_start: 0.7857 (m-80) cc_final: 0.6815 (m-80) REVERT: A 248 ASN cc_start: 0.7775 (m-40) cc_final: 0.7538 (m-40) REVERT: A 287 GLU cc_start: 0.7171 (pp20) cc_final: 0.6750 (pp20) REVERT: A 361 TYR cc_start: 0.8080 (t80) cc_final: 0.7849 (t80) REVERT: A 384 GLU cc_start: 0.7405 (tp30) cc_final: 0.7131 (tp30) REVERT: A 385 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7358 (t80) REVERT: A 492 LEU cc_start: 0.8629 (pt) cc_final: 0.8407 (pt) REVERT: A 580 LYS cc_start: 0.6664 (ttpt) cc_final: 0.6230 (ttpt) REVERT: A 684 GLN cc_start: 0.8000 (tp40) cc_final: 0.7662 (tp40) REVERT: A 687 ASP cc_start: 0.7333 (t70) cc_final: 0.6972 (t0) REVERT: A 730 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: B 21 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8127 (p) REVERT: B 79 ARG cc_start: 0.7380 (ttm170) cc_final: 0.6980 (ttm170) REVERT: B 118 TYR cc_start: 0.8051 (m-10) cc_final: 0.7799 (m-10) REVERT: B 255 TYR cc_start: 0.8382 (m-10) cc_final: 0.7494 (m-10) REVERT: B 370 VAL cc_start: 0.8427 (t) cc_final: 0.8186 (t) REVERT: B 385 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: B 414 GLU cc_start: 0.7165 (tm-30) cc_final: 0.6656 (tm-30) REVERT: B 459 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7372 (tppp) REVERT: B 492 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8293 (pt) REVERT: B 538 ASN cc_start: 0.7206 (p0) cc_final: 0.6842 (p0) REVERT: B 560 ASP cc_start: 0.7329 (m-30) cc_final: 0.7020 (m-30) REVERT: B 681 LYS cc_start: 0.7897 (mptt) cc_final: 0.7691 (mptt) REVERT: B 682 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6280 (mm-30) REVERT: B 687 ASP cc_start: 0.7213 (t70) cc_final: 0.6900 (t70) outliers start: 61 outliers final: 49 residues processed: 346 average time/residue: 0.2936 time to fit residues: 133.5552 Evaluate side-chains 371 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 314 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0770 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 125 optimal weight: 0.0050 chunk 76 optimal weight: 0.5980 overall best weight: 0.2152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 248 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10400 Z= 0.162 Angle : 0.558 7.131 14136 Z= 0.294 Chirality : 0.041 0.165 1718 Planarity : 0.004 0.042 1758 Dihedral : 4.825 50.836 1426 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.67 % Favored : 94.18 % Rotamer: Outliers : 4.63 % Allowed : 19.96 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1322 helix: 1.16 (0.19), residues: 854 sheet: -0.77 (0.88), residues: 36 loop : -1.73 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.002 0.000 HIS A 723 PHE 0.012 0.001 PHE A 115 TYR 0.027 0.002 TYR B 377 ARG 0.011 0.001 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 321 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 66 LYS cc_start: 0.8089 (tptp) cc_final: 0.7626 (tptp) REVERT: A 127 TYR cc_start: 0.8160 (t80) cc_final: 0.7956 (t80) REVERT: A 182 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.6115 (p0) REVERT: A 247 TYR cc_start: 0.7755 (m-80) cc_final: 0.6790 (m-80) REVERT: A 248 ASN cc_start: 0.7652 (m-40) cc_final: 0.7440 (m-40) REVERT: A 287 GLU cc_start: 0.7104 (pp20) cc_final: 0.6621 (pp20) REVERT: A 291 ARG cc_start: 0.7491 (mtm110) cc_final: 0.7257 (mtp180) REVERT: A 384 GLU cc_start: 0.7336 (tp30) cc_final: 0.7062 (tp30) REVERT: A 385 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 432 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7243 (tmm) REVERT: A 475 ASN cc_start: 0.7855 (t0) cc_final: 0.7589 (t0) REVERT: A 492 LEU cc_start: 0.8628 (pt) cc_final: 0.8393 (pt) REVERT: A 556 TYR cc_start: 0.8463 (p90) cc_final: 0.8095 (p90) REVERT: A 580 LYS cc_start: 0.6647 (ttpt) cc_final: 0.6208 (ttpt) REVERT: A 684 GLN cc_start: 0.8012 (tp40) cc_final: 0.7734 (tp40) REVERT: A 685 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7994 (mtm-85) REVERT: A 687 ASP cc_start: 0.7334 (t70) cc_final: 0.6958 (t0) REVERT: A 730 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: B 21 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8086 (p) REVERT: B 39 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7331 (mtm-85) REVERT: B 79 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6879 (ttm170) REVERT: B 97 VAL cc_start: 0.8193 (t) cc_final: 0.7959 (t) REVERT: B 118 TYR cc_start: 0.8003 (m-10) cc_final: 0.7713 (m-10) REVERT: B 255 TYR cc_start: 0.8331 (m-10) cc_final: 0.7476 (m-10) REVERT: B 370 VAL cc_start: 0.8377 (t) cc_final: 0.8152 (t) REVERT: B 385 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 414 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6571 (tm-30) REVERT: B 459 LYS cc_start: 0.7679 (tppp) cc_final: 0.7369 (tppp) REVERT: B 492 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8272 (pt) REVERT: B 560 ASP cc_start: 0.7365 (m-30) cc_final: 0.7058 (m-30) REVERT: B 681 LYS cc_start: 0.7878 (mptt) cc_final: 0.7635 (mptt) REVERT: B 682 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6211 (mm-30) REVERT: B 685 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7573 (mtm180) REVERT: B 687 ASP cc_start: 0.7217 (t70) cc_final: 0.6916 (t70) REVERT: B 717 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7856 (ttm170) outliers start: 52 outliers final: 41 residues processed: 348 average time/residue: 0.2875 time to fit residues: 130.4974 Evaluate side-chains 368 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 319 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 80 optimal weight: 0.0970 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 248 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10400 Z= 0.188 Angle : 0.578 7.208 14136 Z= 0.305 Chirality : 0.042 0.171 1718 Planarity : 0.004 0.043 1758 Dihedral : 4.771 46.966 1426 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.02 % Rotamer: Outliers : 4.63 % Allowed : 20.41 % Favored : 74.96 % 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: 0.38 (0.25), residues: 1322 helix: 1.30 (0.19), residues: 842 sheet: -0.68 (0.89), residues: 36 loop : -1.75 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS A 723 PHE 0.026 0.001 PHE A 130 TYR 0.025 0.002 TYR B 377 ARG 0.009 0.001 ARG A 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 322 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 66 LYS cc_start: 0.8081 (tptp) cc_final: 0.7621 (tptp) REVERT: A 79 ARG cc_start: 0.6980 (mmm-85) cc_final: 0.6780 (mmt90) REVERT: A 127 TYR cc_start: 0.8165 (t80) cc_final: 0.7964 (t80) REVERT: A 182 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6127 (p0) REVERT: A 248 ASN cc_start: 0.7715 (m-40) cc_final: 0.7491 (m-40) REVERT: A 287 GLU cc_start: 0.7102 (pp20) cc_final: 0.6713 (pp20) REVERT: A 323 TYR cc_start: 0.7866 (m-10) cc_final: 0.7657 (m-10) REVERT: A 384 GLU cc_start: 0.7223 (tp30) cc_final: 0.6978 (tp30) REVERT: A 432 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7248 (tmm) REVERT: A 475 ASN cc_start: 0.7871 (t0) cc_final: 0.7474 (t0) REVERT: A 492 LEU cc_start: 0.8632 (pt) cc_final: 0.8404 (pt) REVERT: A 556 TYR cc_start: 0.8460 (p90) cc_final: 0.8111 (p90) REVERT: A 580 LYS cc_start: 0.6668 (ttpt) cc_final: 0.6220 (ttpt) REVERT: A 684 GLN cc_start: 0.7996 (tp40) cc_final: 0.7715 (tp40) REVERT: A 685 ARG cc_start: 0.8203 (mtm180) cc_final: 0.7989 (mtm-85) REVERT: A 687 ASP cc_start: 0.7318 (t70) cc_final: 0.6968 (t0) REVERT: A 730 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: B 21 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8083 (p) REVERT: B 39 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7395 (ttm-80) REVERT: B 79 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6967 (ttm170) REVERT: B 118 TYR cc_start: 0.8032 (m-10) cc_final: 0.7771 (m-10) REVERT: B 255 TYR cc_start: 0.8318 (m-10) cc_final: 0.7495 (m-10) REVERT: B 370 VAL cc_start: 0.8394 (t) cc_final: 0.8162 (t) REVERT: B 385 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: B 414 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6567 (tm-30) REVERT: B 459 LYS cc_start: 0.7688 (tppp) cc_final: 0.7377 (tppp) REVERT: B 492 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8270 (pt) REVERT: B 560 ASP cc_start: 0.7365 (m-30) cc_final: 0.7075 (m-30) REVERT: B 681 LYS cc_start: 0.7884 (mptt) cc_final: 0.7623 (mptt) REVERT: B 682 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6033 (mm-30) REVERT: B 685 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7369 (mtm180) REVERT: B 687 ASP cc_start: 0.7223 (t70) cc_final: 0.6921 (t70) outliers start: 52 outliers final: 38 residues processed: 350 average time/residue: 0.2793 time to fit residues: 128.3099 Evaluate side-chains 363 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 318 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN ** B 696 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.123809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108334 restraints weight = 15476.438| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.06 r_work: 0.3304 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10400 Z= 0.266 Angle : 0.615 7.835 14136 Z= 0.325 Chirality : 0.044 0.187 1718 Planarity : 0.005 0.053 1758 Dihedral : 4.730 46.209 1423 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.28 % Favored : 93.57 % Rotamer: Outliers : 4.37 % Allowed : 20.59 % Favored : 75.04 % 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: 0.14 (0.24), residues: 1322 helix: 1.00 (0.18), residues: 870 sheet: -0.64 (0.90), residues: 36 loop : -1.76 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.003 0.001 HIS B 723 PHE 0.030 0.002 PHE A 385 TYR 0.037 0.002 TYR A 361 ARG 0.012 0.001 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3056.22 seconds wall clock time: 55 minutes 53.91 seconds (3353.91 seconds total)