Starting phenix.real_space_refine on Thu Feb 15 06:53:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtg_27697/02_2024/8dtg_27697.pdb" } resolution = 3.9 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= 1.000 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 80 5.16 5 C 7290 2.51 5 N 1935 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 5985 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 766} Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 5466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5466 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 702} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 4, 'GLU:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 179 Time building chain proxies: 6.32, per 1000 atoms: 0.55 Number of scatterers: 11451 At special positions: 0 Unit cell: (97.68, 99.44, 168.08, 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 80 16.00 O 2146 8.00 N 1935 7.00 C 7290 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: 4.61 Conformation dependent library (CDL) restraints added in 2.2 seconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 71.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.587A pdb=" N LEU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 141 Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.676A pdb=" N ALA A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 185 through 199 removed outlier: 3.832A pdb=" N TYR A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.528A pdb=" N TYR A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 253 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.599A pdb=" N TYR A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 310 through 325 Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.619A pdb=" N CYS A 332 " --> pdb=" O CYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 378 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 497 through 507 removed outlier: 5.305A pdb=" N ALA A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Proline residue: A 504 - end of helix Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.709A pdb=" N LYS A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.853A pdb=" N MET A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 removed outlier: 3.964A pdb=" N SER A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 667 through 681 removed outlier: 3.612A pdb=" N LEU A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 695 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 732 through 735 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 767 through 781 removed outlier: 5.105A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.734A pdb=" N ASP A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 820 removed outlier: 4.238A pdb=" N ARG A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP A 816 " --> pdb=" O MET A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 Processing helix chain 'A' and resid 825 through 846 Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 126 through 141 Processing helix chain 'B' and resid 144 through 166 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.605A pdb=" N TYR B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.966A pdb=" N TYR B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 250 Processing helix chain 'B' and resid 253 through 274 Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.641A pdb=" N PHE B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 445 removed outlier: 3.818A pdb=" N TYR B 443 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 Processing helix chain 'B' and resid 497 through 507 removed outlier: 5.344A pdb=" N ALA B 503 " --> pdb=" O TYR B 499 " (cutoff:3.500A) Proline residue: B 504 - end of helix Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.609A pdb=" N CYS B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 642 removed outlier: 3.677A pdb=" N ALA B 641 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 642 " --> pdb=" O PRO B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 642' Processing helix chain 'B' and resid 647 through 652 removed outlier: 4.051A pdb=" N SER B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 681 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 709 removed outlier: 3.619A pdb=" N LEU B 709 " --> pdb=" O THR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 732 through 735 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 767 through 780 removed outlier: 5.243A pdb=" N GLY B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 774 " --> pdb=" O HIS B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 789 through 803 removed outlier: 3.701A pdb=" N ASP B 803 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 4.194A pdb=" N ARG B 815 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP B 816 " --> pdb=" O MET B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 824 No H-bonds generated for 'chain 'B' and resid 822 through 824' Processing helix chain 'B' and resid 825 through 846 Processing sheet with id=AA1, first strand: chain 'A' and resid 541 through 544 removed outlier: 8.418A pdb=" N VAL A 541 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL A 515 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS A 543 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL A 517 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 483 " --> pdb=" O LYS A 514 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL A 516 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 485 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR A 518 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TYR A 487 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN A 588 " --> pdb=" O TYR A 605 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE A 607 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 590 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ASP A 609 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 716 through 719 removed outlier: 8.462A pdb=" N ASP A 717 " --> pdb=" O SER A 684 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 686 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 719 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 688 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 655 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL A 687 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 657 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS A 689 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 659 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER A 738 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N MET A 763 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA A 787 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 762 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 543 through 544 removed outlier: 8.269A pdb=" N LYS B 543 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 517 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 483 " --> pdb=" O LYS B 514 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL B 516 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 485 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR B 518 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 487 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 484 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 566 " --> pdb=" O THR B 484 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY B 486 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 588 " --> pdb=" O TYR B 605 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE B 607 " --> pdb=" O GLN B 588 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR B 590 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP B 609 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG B 606 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 628 " --> pdb=" O ARG B 606 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR B 608 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 684 through 688 removed outlier: 3.959A pdb=" N SER B 659 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER B 738 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N MET B 763 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 787 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 762 " --> pdb=" O ALA B 787 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2247 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: 3.90 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3763 1.34 - 1.46: 2496 1.46 - 1.58: 5329 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 11708 Sorted by residual: bond pdb=" CG LEU A 155 " pdb=" CD1 LEU A 155 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CA LEU A 288 " pdb=" C LEU A 288 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.34e-02 5.57e+03 1.30e+00 bond pdb=" CG GLN A 435 " pdb=" CD GLN A 435 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" CB TRP A 459 " pdb=" CG TRP A 459 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.15e+00 bond pdb=" CB GLU B 567 " pdb=" CG GLU B 567 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.10e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 275 105.76 - 112.82: 6217 112.82 - 119.89: 4091 119.89 - 126.96: 5264 126.96 - 134.03: 135 Bond angle restraints: 15982 Sorted by residual: angle pdb=" N HIS A 508 " pdb=" CA HIS A 508 " pdb=" CB HIS A 508 " ideal model delta sigma weight residual 110.77 115.71 -4.94 1.63e+00 3.76e-01 9.20e+00 angle pdb=" CA GLN A 435 " pdb=" CB GLN A 435 " pdb=" CG GLN A 435 " ideal model delta sigma weight residual 114.10 119.34 -5.24 2.00e+00 2.50e-01 6.86e+00 angle pdb=" C ILE A 592 " pdb=" CA ILE A 592 " pdb=" CB ILE A 592 " ideal model delta sigma weight residual 111.29 107.13 4.16 1.64e+00 3.72e-01 6.44e+00 angle pdb=" N LEU B 309 " pdb=" CA LEU B 309 " pdb=" C LEU B 309 " ideal model delta sigma weight residual 110.80 116.14 -5.34 2.13e+00 2.20e-01 6.28e+00 angle pdb=" N TRP B 591 " pdb=" CA TRP B 591 " pdb=" C TRP B 591 " ideal model delta sigma weight residual 110.80 116.06 -5.26 2.13e+00 2.20e-01 6.09e+00 ... (remaining 15977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 6376 16.41 - 32.82: 469 32.82 - 49.23: 101 49.23 - 65.63: 12 65.63 - 82.04: 8 Dihedral angle restraints: 6966 sinusoidal: 2441 harmonic: 4525 Sorted by residual: dihedral pdb=" CA PRO A 108 " pdb=" C PRO A 108 " pdb=" N HIS A 109 " pdb=" CA HIS A 109 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CG ARG B 685 " pdb=" CD ARG B 685 " pdb=" NE ARG B 685 " pdb=" CZ ARG B 685 " ideal model delta sinusoidal sigma weight residual -90.00 -134.89 44.89 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA TRP B 591 " pdb=" C TRP B 591 " pdb=" N ILE B 592 " pdb=" CA ILE B 592 " ideal model delta harmonic sigma weight residual -180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1450 0.046 - 0.092: 307 0.092 - 0.138: 67 0.138 - 0.184: 5 0.184 - 0.230: 2 Chirality restraints: 1831 Sorted by residual: chirality pdb=" CA LEU A 155 " pdb=" N LEU A 155 " pdb=" C LEU A 155 " pdb=" CB LEU A 155 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 151 " pdb=" CB LEU A 151 " pdb=" CD1 LEU A 151 " pdb=" CD2 LEU A 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CG LEU A 155 " pdb=" CB LEU A 155 " pdb=" CD1 LEU A 155 " pdb=" CD2 LEU A 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1828 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 393 " 0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 394 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 508 " 0.023 2.00e-02 2.50e+03 2.78e-02 1.16e+01 pdb=" CG HIS A 508 " -0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS A 508 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS A 508 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 508 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 508 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 427 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 428 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " 0.044 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 251 2.69 - 3.24: 12632 3.24 - 3.79: 19196 3.79 - 4.35: 24246 4.35 - 4.90: 38994 Nonbonded interactions: 95319 Sorted by model distance: nonbonded pdb=" OH TYR B 635 " pdb=" OE2 GLU B 752 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR B 569 " pdb=" OG1 THR B 572 " model vdw 2.203 2.440 nonbonded pdb=" OD1 ASN B 442 " pdb=" OH TYR B 594 " model vdw 2.255 2.440 nonbonded pdb=" O SER B 813 " pdb=" OD1 ASP B 816 " model vdw 2.280 3.040 nonbonded pdb=" O ILE A 417 " pdb=" OE1 GLU A 421 " model vdw 2.285 3.040 ... (remaining 95314 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' and ((resid 110 through 117 and (name N or name CA or name C or name \ O or name CB )) or resid 118 through 119 or (resid 120 through 124 and (name N o \ r name CA or name C or name O or name CB )) or (resid 125 through 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 142 or (resi \ d 143 through 149 and (name N or name CA or name C or name O or name CB )) or re \ sid 150 or (resid 151 through 158 and (name N or name CA or name C or name O or \ name CB )) or resid 159 or (resid 160 through 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 or (resid 167 through 170 and (name N or \ name CA or name C or name O or name CB )) or resid 171 or (resid 172 through 18 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 182 through \ 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) or re \ sid 185 through 188 or (resid 189 through 190 and (name N or name CA or name C o \ r name O or name CB )) or resid 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 or (resid 194 through 196 and (name N or \ name CA or name C or name O or name CB )) or resid 197 or (resid 198 through 20 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 202 through \ 203 or (resid 204 through 208 and (name N or name CA or name C or name O or name \ CB )) or resid 209 or (resid 210 through 213 and (name N or name CA or name C o \ r name O or name CB )) or resid 214 or (resid 215 through 216 and (name N or nam \ e CA or name C or name O or name CB )) or resid 217 or (resid 218 through 220 an \ d (name N or name CA or name C or name O or name CB )) or resid 221 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 386 or (resid 387 and (name N or name CA or name C or name O or name \ CB )) or resid 388 through 444 or (resid 445 and (name N or name CA or name C o \ r name O or name CB )) or resid 446 through 501 or (resid 502 through 503 and (n \ ame N or name CA or name C or name O or name CB )) or resid 504 through 526 or ( \ resid 527 and (name N or name CA or name C or name O or name CB )) or resid 528 \ through 555 or (resid 556 and (name N or name CA or name C or name O or name CB \ )) or resid 557 through 563 or (resid 564 and (name N or name CA or name C or na \ me O or name CB )) or resid 565 through 651 or (resid 652 and (name N or name CA \ or name C or name O or name CB )) or resid 653 through 695 or (resid 696 and (n \ ame N or name CA or name C or name O or name CB )) or resid 697 through 713 or ( \ resid 714 and (name N or name CA or name C or name O or name CB )) or resid 715 \ through 729 or (resid 730 through 731 and (name N or name CA or name C or name O \ or name CB )) or resid 732 through 765 or (resid 766 and (name N or name CA or \ name C or name O or name CB )) or resid 767 through 794 or (resid 795 and (name \ N or name CA or name C or name O or name CB )) or resid 796 through 841 or (resi \ d 842 and (name N or name CA or name C or name O or name CB )) or resid 843 thro \ ugh 846)) selection = (chain 'B' and (resid 110 through 125 or (resid 126 through 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 290 or (resid 291 \ and (name N or name CA or name C or name O or name CB )) or resid 292 through 37 \ 7 or (resid 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 through 473 or (resid 474 and (name N or name CA or name C or name O or na \ me CB )) or resid 475 or (resid 476 through 478 and (name N or name CA or name C \ or name O or name CB )) or resid 479 or (resid 480 through 481 and (name N or n \ ame CA or name C or name O or name CB )) or resid 482 through 536 or (resid 537 \ and (name N or name CA or name C or name O or name CB )) or resid 538 through 54 \ 8 or (resid 549 through 550 and (name N or name CA or name C or name O or name C \ B )) or resid 551 or (resid 552 and (name N or name CA or name C or name O or na \ me CB )) or resid 553 through 554 or (resid 555 through 556 and (name N or name \ CA or name C or name O or name CB )) or resid 557 through 560 or (resid 561 and \ (name N or name CA or name C or name O or name CB )) or resid 562 through 575 or \ (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 7 through 617 or (resid 618 and (name N or name CA or name C or name O or name C \ B )) or resid 619 through 629 or (resid 630 through 631 and (name N or name CA o \ r name C or name O or name CB )) or resid 632 through 644 or (resid 645 and (nam \ e N or name CA or name C or name O or name CB )) or resid 646 through 671 or (re \ sid 672 and (name N or name CA or name C or name O or name CB )) or resid 673 th \ rough 683 or (resid 684 and (name N or name CA or name C or name O or name CB )) \ or resid 685 through 689 or (resid 690 and (name N or name CA or name C or name \ O or name CB )) or resid 691 through 706 or (resid 707 and (name N or name CA o \ r name C or name O or name CB )) or resid 708 through 721 or (resid 722 through \ 724 and (name N or name CA or name C or name O or name CB )) or resid 725 throug \ h 727 or (resid 728 and (name N or name CA or name C or name O or name CB )) or \ resid 729 through 734 or (resid 735 and (name N or name CA or name C or name O o \ r name CB )) or resid 736 through 751 or (resid 752 and (name N or name CA or na \ me C or name O or name CB )) or resid 753 through 845 or (resid 846 and (name N \ or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 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: 0.010 Extract box with map and model: 12.180 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.390 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.004 0.048 11708 Z= 0.242 Angle : 0.632 6.968 15982 Z= 0.341 Chirality : 0.040 0.230 1831 Planarity : 0.006 0.091 2070 Dihedral : 12.356 82.042 4062 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.05 (0.21), residues: 1535 helix: 0.97 (0.16), residues: 1039 sheet: -0.69 (0.56), residues: 105 loop : -2.28 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 591 HIS 0.033 0.002 HIS A 508 PHE 0.033 0.002 PHE A 463 TYR 0.053 0.002 TYR A 837 ARG 0.009 0.001 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.266 Fit side-chains REVERT: A 491 ASP cc_start: 0.8120 (m-30) cc_final: 0.7752 (m-30) REVERT: A 566 VAL cc_start: 0.8467 (t) cc_final: 0.7994 (t) REVERT: A 580 MET cc_start: 0.8624 (mtt) cc_final: 0.8381 (mtt) REVERT: A 818 MET cc_start: 0.8215 (ppp) cc_final: 0.7831 (ptt) REVERT: B 209 TYR cc_start: 0.8219 (m-80) cc_final: 0.7870 (m-80) REVERT: B 473 TRP cc_start: 0.7923 (m-90) cc_final: 0.7711 (m-90) REVERT: B 494 THR cc_start: 0.8122 (p) cc_final: 0.7835 (t) REVERT: B 793 TYR cc_start: 0.8215 (t80) cc_final: 0.7797 (t80) REVERT: B 837 TYR cc_start: 0.8642 (m-10) cc_final: 0.8417 (m-10) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1716 time to fit residues: 51.2183 Evaluate side-chains 162 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.0470 chunk 72 optimal weight: 0.0870 chunk 89 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 167 ASN A 445 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.184 Angle : 0.562 8.670 15982 Z= 0.286 Chirality : 0.039 0.137 1831 Planarity : 0.004 0.055 2070 Dihedral : 3.764 16.697 1670 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.16 % Allowed : 7.03 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.60 (0.22), residues: 1535 helix: 2.08 (0.16), residues: 1035 sheet: -0.42 (0.53), residues: 113 loop : -1.31 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 591 HIS 0.018 0.001 HIS A 508 PHE 0.016 0.002 PHE A 463 TYR 0.032 0.002 TYR A 837 ARG 0.003 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8154 (m-30) cc_final: 0.7708 (m-30) REVERT: A 632 PHE cc_start: 0.8047 (p90) cc_final: 0.7182 (p90) REVERT: A 633 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8444 (mp) REVERT: B 209 TYR cc_start: 0.8168 (m-80) cc_final: 0.7927 (m-80) REVERT: B 231 LYS cc_start: 0.8784 (tttm) cc_final: 0.8498 (ttmt) REVERT: B 244 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 473 TRP cc_start: 0.7887 (m-90) cc_final: 0.7677 (m-90) REVERT: B 494 THR cc_start: 0.8075 (p) cc_final: 0.7809 (t) REVERT: B 657 PHE cc_start: 0.7261 (m-80) cc_final: 0.6783 (m-10) outliers start: 13 outliers final: 8 residues processed: 193 average time/residue: 0.2038 time to fit residues: 59.6422 Evaluate side-chains 169 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 38 optimal weight: 0.0270 chunk 139 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 0.0470 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11708 Z= 0.156 Angle : 0.542 12.119 15982 Z= 0.267 Chirality : 0.038 0.155 1831 Planarity : 0.004 0.059 2070 Dihedral : 3.675 17.661 1670 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.42 % Allowed : 10.23 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.95 (0.22), residues: 1535 helix: 2.32 (0.16), residues: 1034 sheet: -0.23 (0.53), residues: 113 loop : -1.13 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 591 HIS 0.013 0.001 HIS A 508 PHE 0.012 0.001 PHE A 463 TYR 0.025 0.001 TYR A 837 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8174 (m-30) cc_final: 0.7762 (m-30) REVERT: B 231 LYS cc_start: 0.8757 (tttm) cc_final: 0.8530 (ttmm) REVERT: B 494 THR cc_start: 0.8102 (p) cc_final: 0.7848 (t) REVERT: B 729 MET cc_start: 0.8645 (mmm) cc_final: 0.8438 (mmm) outliers start: 16 outliers final: 11 residues processed: 181 average time/residue: 0.1874 time to fit residues: 52.4063 Evaluate side-chains 166 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 763 MET Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 0.0970 chunk 132 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11708 Z= 0.150 Angle : 0.534 12.040 15982 Z= 0.259 Chirality : 0.038 0.222 1831 Planarity : 0.004 0.060 2070 Dihedral : 3.640 18.141 1670 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.60 % Allowed : 11.74 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 2.07 (0.23), residues: 1535 helix: 2.41 (0.16), residues: 1034 sheet: -0.15 (0.54), residues: 109 loop : -1.09 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 591 HIS 0.011 0.001 HIS A 508 PHE 0.015 0.001 PHE A 632 TYR 0.021 0.001 TYR A 837 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 ASP cc_start: 0.8222 (m-30) cc_final: 0.7830 (m-30) REVERT: A 729 MET cc_start: 0.7698 (mmp) cc_final: 0.7289 (mmm) REVERT: B 209 TYR cc_start: 0.8183 (m-80) cc_final: 0.7973 (m-80) REVERT: B 231 LYS cc_start: 0.8723 (tttm) cc_final: 0.8488 (ttmm) REVERT: B 244 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8109 (mm-30) REVERT: B 494 THR cc_start: 0.8099 (p) cc_final: 0.7835 (t) REVERT: B 709 LEU cc_start: 0.8683 (mm) cc_final: 0.8422 (mm) REVERT: B 729 MET cc_start: 0.8680 (mmm) cc_final: 0.8420 (mmm) outliers start: 18 outliers final: 14 residues processed: 184 average time/residue: 0.1876 time to fit residues: 54.0383 Evaluate side-chains 171 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 767 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 225 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11708 Z= 0.390 Angle : 0.666 10.381 15982 Z= 0.341 Chirality : 0.042 0.240 1831 Planarity : 0.005 0.063 2070 Dihedral : 4.028 18.788 1670 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.05 % Allowed : 12.63 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.61 (0.22), residues: 1535 helix: 1.96 (0.16), residues: 1038 sheet: -0.10 (0.55), residues: 110 loop : -1.06 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 591 HIS 0.011 0.001 HIS A 508 PHE 0.023 0.002 PHE A 253 TYR 0.019 0.002 TYR A 318 ARG 0.004 0.001 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8562 (t80) REVERT: A 729 MET cc_start: 0.7973 (mmp) cc_final: 0.7723 (mmp) REVERT: B 231 LYS cc_start: 0.8820 (tttm) cc_final: 0.8557 (ttmm) REVERT: B 244 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8243 (mm-30) REVERT: B 494 THR cc_start: 0.8094 (p) cc_final: 0.7790 (t) REVERT: B 633 LEU cc_start: 0.9227 (mt) cc_final: 0.8935 (mt) REVERT: B 709 LEU cc_start: 0.8659 (mm) cc_final: 0.8369 (mm) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.1771 time to fit residues: 52.0970 Evaluate side-chains 174 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 700 GLN Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 36 optimal weight: 0.4980 chunk 148 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 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 367 ASN A 402 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11708 Z= 0.169 Angle : 0.584 13.449 15982 Z= 0.282 Chirality : 0.039 0.329 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.846 17.718 1670 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.78 % Allowed : 14.41 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.97 (0.23), residues: 1535 helix: 2.25 (0.16), residues: 1038 sheet: 0.07 (0.55), residues: 110 loop : -0.98 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 591 HIS 0.009 0.001 HIS A 508 PHE 0.012 0.001 PHE B 400 TYR 0.015 0.001 TYR A 837 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8506 (t80) REVERT: A 729 MET cc_start: 0.7952 (mmp) cc_final: 0.7618 (mmp) REVERT: B 231 LYS cc_start: 0.8722 (tttm) cc_final: 0.8491 (ttmm) REVERT: B 494 THR cc_start: 0.8078 (p) cc_final: 0.7774 (t) REVERT: B 709 LEU cc_start: 0.8602 (mm) cc_final: 0.8336 (mm) REVERT: B 817 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8987 (pp) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.1792 time to fit residues: 50.6190 Evaluate side-chains 177 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 817 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11708 Z= 0.189 Angle : 0.579 12.717 15982 Z= 0.278 Chirality : 0.039 0.333 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.778 17.885 1670 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.78 % Allowed : 15.21 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 2.01 (0.23), residues: 1535 helix: 2.29 (0.16), residues: 1039 sheet: 0.05 (0.55), residues: 110 loop : -0.99 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 591 HIS 0.008 0.001 HIS A 508 PHE 0.008 0.001 PHE B 531 TYR 0.015 0.001 TYR A 837 ARG 0.002 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 729 MET cc_start: 0.8028 (mmp) cc_final: 0.7669 (mmp) REVERT: B 244 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 494 THR cc_start: 0.8094 (p) cc_final: 0.7779 (t) REVERT: B 709 LEU cc_start: 0.8570 (mm) cc_final: 0.8295 (mm) REVERT: B 752 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 754 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9159 (mm) outliers start: 20 outliers final: 15 residues processed: 184 average time/residue: 0.1901 time to fit residues: 55.5214 Evaluate side-chains 179 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 367 ASN A 402 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11708 Z= 0.181 Angle : 0.604 13.360 15982 Z= 0.285 Chirality : 0.040 0.347 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.769 17.385 1670 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.69 % Allowed : 16.73 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 2.03 (0.23), residues: 1535 helix: 2.31 (0.16), residues: 1039 sheet: 0.06 (0.52), residues: 116 loop : -1.04 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 591 HIS 0.008 0.001 HIS A 508 PHE 0.008 0.001 PHE A 322 TYR 0.014 0.001 TYR A 837 ARG 0.002 0.000 ARG B 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.363 Fit side-chains REVERT: A 463 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8476 (t80) REVERT: A 729 MET cc_start: 0.8047 (mmp) cc_final: 0.7686 (mmp) REVERT: A 812 MET cc_start: 0.8760 (mmm) cc_final: 0.8520 (mmp) REVERT: A 841 TRP cc_start: 0.7615 (t-100) cc_final: 0.7008 (t-100) REVERT: B 244 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 494 THR cc_start: 0.8091 (p) cc_final: 0.7776 (t) REVERT: B 709 LEU cc_start: 0.8560 (mm) cc_final: 0.8275 (mm) REVERT: B 754 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9147 (mm) outliers start: 19 outliers final: 15 residues processed: 186 average time/residue: 0.1815 time to fit residues: 52.8840 Evaluate side-chains 179 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 726 HIS Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 141 optimal weight: 0.0020 chunk 82 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11708 Z= 0.247 Angle : 0.619 11.560 15982 Z= 0.299 Chirality : 0.041 0.344 1831 Planarity : 0.004 0.064 2070 Dihedral : 3.856 18.188 1670 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.78 % Allowed : 16.81 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.89 (0.23), residues: 1535 helix: 2.23 (0.16), residues: 1038 sheet: -0.14 (0.52), residues: 116 loop : -1.10 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 591 HIS 0.009 0.001 HIS A 768 PHE 0.010 0.001 PHE A 322 TYR 0.016 0.001 TYR A 407 ARG 0.002 0.000 ARG B 811 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.300 Fit side-chains REVERT: A 429 ASP cc_start: 0.7866 (p0) cc_final: 0.7655 (p0) REVERT: A 463 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8490 (t80) REVERT: A 729 MET cc_start: 0.8148 (mmp) cc_final: 0.7744 (mmp) REVERT: A 812 MET cc_start: 0.8816 (mmm) cc_final: 0.8576 (mmp) REVERT: A 818 MET cc_start: 0.7806 (ppp) cc_final: 0.7306 (ppp) REVERT: A 841 TRP cc_start: 0.7675 (t-100) cc_final: 0.7047 (t-100) REVERT: B 244 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 494 THR cc_start: 0.8062 (p) cc_final: 0.7752 (t) REVERT: B 709 LEU cc_start: 0.8612 (mm) cc_final: 0.8338 (mm) REVERT: B 754 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9149 (mm) outliers start: 20 outliers final: 14 residues processed: 174 average time/residue: 0.1738 time to fit residues: 47.8035 Evaluate side-chains 178 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11708 Z= 0.194 Angle : 0.613 13.693 15982 Z= 0.291 Chirality : 0.040 0.346 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.800 17.176 1670 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.60 % Allowed : 17.35 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.93 (0.23), residues: 1535 helix: 2.27 (0.16), residues: 1040 sheet: -0.17 (0.52), residues: 116 loop : -1.12 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 591 HIS 0.010 0.001 HIS A 768 PHE 0.012 0.001 PHE B 531 TYR 0.013 0.001 TYR A 837 ARG 0.002 0.000 ARG A 811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.7841 (m-80) cc_final: 0.7618 (m-10) REVERT: A 189 TYR cc_start: 0.7925 (m-80) cc_final: 0.7676 (m-10) REVERT: A 429 ASP cc_start: 0.7857 (p0) cc_final: 0.7631 (p0) REVERT: A 463 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8497 (t80) REVERT: A 729 MET cc_start: 0.8097 (mmp) cc_final: 0.7707 (mmp) REVERT: A 763 MET cc_start: 0.8137 (ptm) cc_final: 0.7850 (ppp) REVERT: A 812 MET cc_start: 0.8843 (mmm) cc_final: 0.8555 (mmp) REVERT: A 818 MET cc_start: 0.7777 (ppp) cc_final: 0.7374 (ppp) REVERT: A 841 TRP cc_start: 0.7685 (t-100) cc_final: 0.7063 (t-100) REVERT: B 494 THR cc_start: 0.8098 (p) cc_final: 0.7775 (t) REVERT: B 567 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 709 LEU cc_start: 0.8607 (mm) cc_final: 0.8344 (mm) REVERT: B 711 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7119 (tt) REVERT: B 754 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9144 (mm) outliers start: 18 outliers final: 14 residues processed: 178 average time/residue: 0.1867 time to fit residues: 51.6148 Evaluate side-chains 177 residues out of total 1297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 463 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 0.0000 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 402 ASN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 ASN B 402 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081812 restraints weight = 31008.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083221 restraints weight = 16886.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.084332 restraints weight = 10704.526| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11708 Z= 0.177 Angle : 0.620 14.064 15982 Z= 0.293 Chirality : 0.040 0.336 1831 Planarity : 0.004 0.063 2070 Dihedral : 3.811 17.041 1670 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.69 % Allowed : 17.53 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1.96 (0.23), residues: 1535 helix: 2.30 (0.16), residues: 1040 sheet: -0.20 (0.52), residues: 116 loop : -1.11 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 591 HIS 0.010 0.001 HIS A 768 PHE 0.008 0.001 PHE A 322 TYR 0.048 0.001 TYR A 230 ARG 0.002 0.000 ARG B 558 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.48 seconds wall clock time: 46 minutes 15.92 seconds (2775.92 seconds total)