Starting phenix.real_space_refine on Thu Jul 31 18:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.map" model { file = "/net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr9_49726/07_2025/9nr9_49726.cif" } resolution = 4.22 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= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 81 5.16 5 C 8870 2.51 5 N 2176 2.21 5 O 2536 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13679 Number of models: 1 Model: "" Number of chains: 10 Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1327 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1325 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2753 Classifications: {'peptide': 381} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2696 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 14, 'TRANS': 364} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2752 Classifications: {'peptide': 379} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PTRANS': 12, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2718 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.09, per 1000 atoms: 0.66 Number of scatterers: 13679 At special positions: 0 Unit cell: (107.16, 125.96, 133.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 81 16.00 P 4 15.00 F 12 9.00 O 2536 8.00 N 2176 7.00 C 8870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 775 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 720 " - pdb=" SG CYS D 775 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.0 seconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3406 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 15 sheets defined 56.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 4.203A pdb=" N ILE F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 4.088A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 removed outlier: 4.194A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 28 Processing helix chain 'H' and resid 94 through 105 Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.770A pdb=" N ILE H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 162 Processing helix chain 'H' and resid 178 through 208 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.790A pdb=" N PHE A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.651A pdb=" N GLU A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 432 " --> pdb=" O ILE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.661A pdb=" N SER A 512 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.690A pdb=" N LEU A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 543 removed outlier: 4.004A pdb=" N MET A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 626 removed outlier: 4.141A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.774A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.620A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.650A pdb=" N GLY A 685 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 815 removed outlier: 4.098A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 439 removed outlier: 3.792A pdb=" N ILE B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.513A pdb=" N TYR B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 525 through 549 removed outlier: 4.188A pdb=" N MET B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 628 removed outlier: 3.605A pdb=" N ARG B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 645 removed outlier: 4.062A pdb=" N THR B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.593A pdb=" N SER B 678 " --> pdb=" O THR B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 698 Processing helix chain 'B' and resid 708 through 716 removed outlier: 3.807A pdb=" N GLN B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 758 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 794 through 820 removed outlier: 3.898A pdb=" N PHE B 798 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 820 " --> pdb=" O PHE B 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.547A pdb=" N GLN C 410 " --> pdb=" O ASN C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.701A pdb=" N GLY C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 509 through 514 removed outlier: 3.581A pdb=" N PHE C 513 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 514 " --> pdb=" O VAL C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 514' Processing helix chain 'C' and resid 518 through 543 removed outlier: 3.554A pdb=" N SER C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 625 Processing helix chain 'C' and resid 632 through 639 removed outlier: 3.597A pdb=" N THR C 639 " --> pdb=" O LEU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 673 removed outlier: 3.670A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 673 " --> pdb=" O TYR C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 712 removed outlier: 4.220A pdb=" N GLN C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 712 " --> pdb=" O ILE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 753 removed outlier: 3.705A pdb=" N ASN C 743 " --> pdb=" O ARG C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 Processing helix chain 'C' and resid 788 through 815 Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 426 through 439 Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 524 through 547 removed outlier: 3.643A pdb=" N ARG D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 629 Processing helix chain 'D' and resid 638 through 644 Processing helix chain 'D' and resid 655 through 663 removed outlier: 4.269A pdb=" N ARG D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 708 through 715 Processing helix chain 'D' and resid 744 through 759 Processing helix chain 'D' and resid 760 through 770 Processing helix chain 'D' and resid 794 through 819 removed outlier: 4.161A pdb=" N PHE D 798 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 799 " --> pdb=" O ALA D 795 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.727A pdb=" N LEU F 34 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 78 through 79 removed outlier: 3.775A pdb=" N CYS H 67 " --> pdb=" O HIS H 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS H 60 " --> pdb=" O CYS H 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.190A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 486 through 487 removed outlier: 3.928A pdb=" N ASP A 486 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 732 " --> pdb=" O ASP A 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 498 through 501 removed outlier: 4.131A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 719 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AA7, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.626A pdb=" N GLU B 424 " --> pdb=" O MET B 409 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 502 through 505 Processing sheet with id=AA9, first strand: chain 'C' and resid 391 through 394 Processing sheet with id=AB1, first strand: chain 'C' and resid 486 through 487 removed outlier: 3.920A pdb=" N ASP C 486 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.342A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 445 through 446 removed outlier: 6.013A pdb=" N VAL D 399 " --> pdb=" O ALA D 445 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 400 " --> pdb=" O ILE D 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 408 through 410 Processing sheet with id=AB5, first strand: chain 'D' and resid 492 through 493 removed outlier: 3.506A pdb=" N ASP D 492 " --> pdb=" O THR D 738 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 684 through 685 removed outlier: 8.498A pdb=" N THR D 685 " --> pdb=" O TYR D 649 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR D 651 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU D 652 " --> pdb=" O LEU D 705 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N GLU D 707 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE D 704 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET D 505 " --> pdb=" O PHE D 704 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET D 498 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY D 733 " --> pdb=" O MET D 498 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU D 500 " --> pdb=" O SER D 731 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER D 731 " --> pdb=" O LEU D 500 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2307 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: 3.79 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4249 1.34 - 1.48: 3791 1.48 - 1.62: 5799 1.62 - 1.76: 0 1.76 - 1.90: 136 Bond restraints: 13975 Sorted by residual: bond pdb=" C ASP B 521 " pdb=" N PRO B 522 " ideal model delta sigma weight residual 1.326 1.361 -0.035 1.44e-02 4.82e+03 5.92e+00 bond pdb=" CG1 ILE B 531 " pdb=" CD1 ILE B 531 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.39e+00 bond pdb=" CB LYS A 489 " pdb=" CG LYS A 489 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" CB LYS B 495 " pdb=" CG LYS B 495 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C GLU A 674 " pdb=" N PRO A 675 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 ... (remaining 13970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 18675 2.55 - 5.10: 310 5.10 - 7.65: 72 7.65 - 10.20: 15 10.20 - 12.75: 5 Bond angle restraints: 19077 Sorted by residual: angle pdb=" N PRO D 777 " pdb=" CA PRO D 777 " pdb=" CB PRO D 777 " ideal model delta sigma weight residual 103.51 110.16 -6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N PRO D 747 " pdb=" CA PRO D 747 " pdb=" CB PRO D 747 " ideal model delta sigma weight residual 103.23 110.01 -6.78 1.07e+00 8.73e-01 4.02e+01 angle pdb=" N PRO B 747 " pdb=" CA PRO B 747 " pdb=" CB PRO B 747 " ideal model delta sigma weight residual 103.23 109.98 -6.75 1.07e+00 8.73e-01 3.98e+01 angle pdb=" N PRO B 777 " pdb=" CA PRO B 777 " pdb=" CB PRO B 777 " ideal model delta sigma weight residual 103.44 110.08 -6.64 1.12e+00 7.97e-01 3.52e+01 angle pdb=" C TRP D 528 " pdb=" N MET D 529 " pdb=" CA MET D 529 " ideal model delta sigma weight residual 121.58 112.07 9.51 1.95e+00 2.63e-01 2.38e+01 ... (remaining 19072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 7406 17.41 - 34.82: 563 34.82 - 52.23: 105 52.23 - 69.64: 13 69.64 - 87.06: 5 Dihedral angle restraints: 8092 sinusoidal: 2748 harmonic: 5344 Sorted by residual: dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 156.88 -63.88 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 152.05 -59.05 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual -86.00 -136.97 50.97 1 1.00e+01 1.00e-02 3.56e+01 ... (remaining 8089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1823 0.058 - 0.116: 361 0.116 - 0.174: 47 0.174 - 0.232: 9 0.232 - 0.290: 3 Chirality restraints: 2243 Sorted by residual: chirality pdb=" CB VAL B 532 " pdb=" CA VAL B 532 " pdb=" CG1 VAL B 532 " pdb=" CG2 VAL B 532 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE B 478 " pdb=" CA ILE B 478 " pdb=" CG1 ILE B 478 " pdb=" CG2 ILE B 478 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA PRO D 777 " pdb=" N PRO D 777 " pdb=" C PRO D 777 " pdb=" CB PRO D 777 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2240 not shown) Planarity restraints: 2354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 141 " 0.017 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE F 141 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE F 141 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE F 141 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE F 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 141 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 712 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO A 713 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 405 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO D 406 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 406 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 406 " -0.034 5.00e-02 4.00e+02 ... (remaining 2351 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3818 2.81 - 3.33: 13394 3.33 - 3.85: 22132 3.85 - 4.38: 22872 4.38 - 4.90: 40052 Nonbonded interactions: 102268 Sorted by model distance: nonbonded pdb=" NH1 ARG F 37 " pdb=" O ASN F 172 " model vdw 2.281 3.120 nonbonded pdb=" O GLY B 515 " pdb=" OG SER B 518 " model vdw 2.287 3.040 nonbonded pdb=" O CYS C 811 " pdb=" OG SER C 814 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU D 404 " pdb=" OH TYR D 452 " model vdw 2.323 3.040 nonbonded pdb=" OD2 ASP D 456 " pdb=" OG1 THR D 459 " model vdw 2.337 3.040 ... (remaining 102263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 396 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 400 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or (resid 405 through 407 and (name \ N or name CA or name C or name O or name CB )) or (resid 411 through 414 and (n \ ame N or name CA or name C or name O or name CB )) or resid 415 or resid 417 thr \ ough 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid \ 436 or resid 440 through 441 or resid 443 through 449 or (resid 450 and (name N \ or name CA or name C or name O or name CB )) or resid 452 through 454 or resid \ 456 through 466 or resid 468 or resid 471 or resid 473 through 493 or (resid 494 \ and (name N or name CA or name C or name O or name CB )) or resid 495 through 5 \ 05 or (resid 506 through 507 and (name N or name CA or name C or name O or name \ CB )) or resid 508 through 510 or (resid 511 and (name N or name CA or name C or \ name O or name CB )) or resid 512 through 514 or (resid 515 and (name N or name \ CA or name C or name O or name CB )) or resid 516 through 541 or resid 592 thro \ ugh 594 or (resid 595 and (name N or name CA or name C or name O or name CB )) o \ r resid 596 through 624 or (resid 625 and (name N or name CA or name C or name O \ or name CB )) or resid 626 through 632 or (resid 633 and (name N or name CA or \ name C or name O or name CB )) or resid 634 or (resid 635 through 638 and (name \ N or name CA or name C or name O or name CB )) or resid 639 through 642 or (resi \ d 643 and (name N or name CA or name C or name O or name CB )) or resid 644 thro \ ugh 646 or resid 649 through 654 or (resid 655 through 657 and (name N or name C \ A or name C or name O or name CB )) or resid 658 through 662 or resid 664 throug \ h 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or \ resid 672 through 677 or (resid 678 and (name N or name CA or name C or name O o \ r name CB )) or resid 680 through 682 or resid 684 through 685 or (resid 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 690 \ through 691 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 92 through 695 or resid 697 or resid 699 through 700 or (resid 701 and (name N o \ r name CA or name C or name O or name CB )) or resid 702 through 707 or resid 70 \ 9 through 716 or (resid 717 through 718 and (name N or name CA or name C or name \ O or name CB )) or resid 719 through 729 or resid 731 through 733 or (resid 734 \ and (name N or name CA or name C or name O or name CB )) or resid 735 through 7 \ 36 or resid 738 through 739 or (resid 741 and (name N or name CA or name C or na \ me O or name CB )) or resid 742 through 747 or (resid 748 and (name N or name CA \ or name C or name O or name CB )) or resid 749 or (resid 751 and (name N or nam \ e CA or name C or name O or name CB )) or resid 753 or resid 755 through 760 or \ (resid 761 and (name N or name CA or name C or name O or name CB )) or resid 762 \ through 770 or resid 776 through 780 or (resid 781 through 782 and (name N or n \ ame CA or name C or name O or name CB )) or resid 783 through 795 or resid 797 t \ hrough 808 or (resid 809 and (name N or name CA or name C or name O or name CB ) \ ) or resid 810 through 812 or (resid 813 and (name N or name CA or name C or nam \ e O or name CB )) or resid 901)) selection = (chain 'B' and (resid 399 through 402 or resid 404 or resid 406 through 409 or ( \ resid 411 through 413 and (name N or name CA or name C or name O or name CB )) o \ r resid 417 through 421 or (resid 423 and (name N or name CA or name C or name O \ or name CB )) or resid 424 through 428 or resid 430 through 431 or resid 433 th \ rough 437 or resid 439 or resid 442 or resid 446 through 447 or resid 449 throug \ h 456 or (resid 458 and (name N or name CA or name C or name O or name CB )) or \ resid 459 through 460 or resid 462 through 472 or resid 474 or resid 477 or resi \ d 479 through 499 or (resid 500 and (name N or name CA or name C or name O or na \ me CB )) or resid 501 through 509 or (resid 510 through 513 and (name N or name \ CA or name C or name O or name CB )) or resid 514 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 547 or \ resid 598 through 628 or (resid 629 and (name N or name CA or name C or name O \ or name CB )) or resid 630 or (resid 631 and (name N or name CA or name C or nam \ e O or name CB )) or resid 632 through 643 or (resid 644 and (name N or name CA \ or name C or name O or name CB )) or resid 645 through 648 or (resid 649 and (na \ me N or name CA or name C or name O or name CB )) or resid 650 through 652 or re \ sid 655 through 668 or (resid 670 through 671 and (name N or name CA or name C o \ r name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or nam \ e CA or name C or name O or name CB )) or resid 678 through 683 or (resid 684 an \ d (name N or name CA or name C or name O or name CB )) or resid 686 through 688 \ or resid 690 through 691 or resid 694 through 701 or resid 703 or resid 705 thro \ ugh 706 or (resid 707 and (name N or name CA or name C or name O or name CB )) o \ r resid 708 through 713 or resid 715 through 722 or (resid 723 through 724 and ( \ name N or name CA or name C or name O or name CB )) or resid 725 through 735 or \ resid 737 through 739 or (resid 740 and (name N or name CA or name C or name O o \ r name CB )) or resid 741 through 742 or resid 744 through 745 or resid 747 thro \ ugh 755 or resid 757 or resid 759 or resid 761 through 765 or (resid 766 through \ 767 and (name N or name CA or name C or name O or name CB )) or resid 768 throu \ gh 776 or resid 782 through 785 or (resid 786 through 788 and (name N or name CA \ or name C or name O or name CB )) or resid 789 through 801 or resid 803 through \ 814 or (resid 815 and (name N or name CA or name C or name O or name CB )) or r \ esid 816 through 819 or resid 901)) selection = (chain 'C' and (resid 393 through 396 or (resid 398 and (name N or name CA or na \ me C or name O or name CB )) or resid 400 through 402 or (resid 403 and (name N \ or name CA or name C or name O or name CB )) or (resid 405 through 407 and (name \ N or name CA or name C or name O or name CB )) or resid 411 through 415 or (res \ id 417 and (name N or name CA or name C or name O or name CB )) or resid 418 thr \ ough 422 or resid 424 through 425 or resid 427 through 431 or resid 433 or resid \ 436 or resid 440 through 441 or resid 443 through 448 or (resid 449 through 450 \ and (name N or name CA or name C or name O or name CB )) or (resid 452 and (nam \ e N or name CA or name C or name O or name CB )) or resid 453 through 454 or res \ id 456 through 458 or (resid 459 and (name N or name CA or name C or name O or n \ ame CB )) or resid 460 through 466 or resid 468 or resid 471 or resid 473 throug \ h 493 or (resid 494 and (name N or name CA or name C or name O or name CB )) or \ resid 495 through 505 or (resid 506 through 507 and (name N or name CA or name C \ or name O or name CB )) or resid 508 through 514 or (resid 515 and (name N or n \ ame CA or name C or name O or name CB )) or resid 516 through 541 or resid 592 t \ hrough 594 or (resid 595 and (name N or name CA or name C or name O or name CB ) \ ) or resid 596 through 624 or (resid 625 and (name N or name CA or name C or nam \ e O or name CB )) or resid 626 through 629 or (resid 630 and (name N or name CA \ or name C or name O or name CB )) or resid 631 through 632 or (resid 633 and (na \ me N or name CA or name C or name O or name CB )) or resid 634 or (resid 635 thr \ ough 638 and (name N or name CA or name C or name O or name CB )) or resid 639 t \ hrough 646 or resid 649 through 654 or (resid 655 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 662 or resid 664 thr \ ough 670 or resid 672 through 678 or resid 680 through 682 or resid 684 through \ 685 or (resid 688 and (name N or name CA or name C or name O or name CB )) or re \ sid 689 or (resid 690 through 691 and (name N or name CA or name C or name O or \ name CB )) or resid 692 through 695 or resid 697 or resid 699 through 707 or res \ id 709 through 716 or (resid 717 through 718 and (name N or name CA or name C or \ name O or name CB )) or resid 719 through 729 or resid 731 through 736 or resid \ 738 through 739 or (resid 741 and (name N or name CA or name C or name O or nam \ e CB )) or resid 742 through 747 or (resid 748 and (name N or name CA or name C \ or name O or name CB )) or resid 749 or (resid 751 and (name N or name CA or nam \ e C or name O or name CB )) or resid 753 or resid 755 through 760 or (resid 761 \ and (name N or name CA or name C or name O or name CB )) or resid 762 through 77 \ 0 or resid 776 through 795 or resid 797 through 812 or (resid 813 and (name N or \ name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 399 through 402 or (resid 404 and (name N or name CA or na \ me C or name O or name CB )) or resid 406 through 408 or (resid 409 and (name N \ or name CA or name C or name O or name CB )) or (resid 411 through 413 and (name \ N or name CA or name C or name O or name CB )) or (resid 417 through 418 and (n \ ame N or name CA or name C or name O or name CB )) or resid 419 or (resid 420 an \ d (name N or name CA or name C or name O or name CB )) or resid 421 or (resid 42 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 424 through \ 428 or resid 430 through 431 or resid 433 through 437 or resid 439 or resid 442 \ or resid 446 through 447 or resid 449 through 454 or (resid 455 through 456 and \ (name N or name CA or name C or name O or name CB )) or (resid 458 and (name N o \ r name CA or name C or name O or name CB )) or resid 459 through 460 or resid 46 \ 2 through 464 or (resid 465 and (name N or name CA or name C or name O or name C \ B )) or resid 466 through 472 or resid 474 or resid 477 or resid 479 through 509 \ or (resid 510 through 513 and (name N or name CA or name C or name O or name CB \ )) or resid 514 through 516 or (resid 517 and (name N or name CA or name C or n \ ame O or name CB )) or resid 518 through 547 or resid 598 through 628 or (resid \ 629 and (name N or name CA or name C or name O or name CB )) or resid 630 throug \ h 640 or (resid 641 through 644 and (name N or name CA or name C or name O or na \ me CB )) or resid 645 or (resid 646 and (name N or name CA or name C or name O o \ r name CB )) or resid 647 through 648 or (resid 649 and (name N or name CA or na \ me C or name O or name CB )) or resid 650 through 652 or resid 655 through 660 o \ r (resid 661 through 663 and (name N or name CA or name C or name O or name CB ) \ ) or resid 664 through 668 or (resid 670 through 671 and (name N or name CA or n \ ame C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N \ or name CA or name C or name O or name CB )) or resid 678 through 683 or (resid \ 684 and (name N or name CA or name C or name O or name CB )) or resid 686 throu \ gh 688 or resid 690 through 691 or (resid 694 and (name N or name CA or name C o \ r name O or name CB )) or resid 695 or (resid 696 through 697 and (name N or nam \ e CA or name C or name O or name CB )) or resid 698 through 701 or resid 703 or \ resid 705 through 706 or (resid 707 and (name N or name CA or name C or name O o \ r name CB )) or resid 708 through 713 or resid 715 through 723 or (resid 724 and \ (name N or name CA or name C or name O or name CB )) or resid 725 through 735 o \ r resid 737 through 739 or (resid 740 and (name N or name CA or name C or name O \ or name CB )) or resid 741 through 742 or resid 744 through 745 or resid 747 th \ rough 753 or (resid 754 and (name N or name CA or name C or name O or name CB )) \ or resid 755 or resid 757 or resid 759 or resid 761 through 765 or (resid 766 t \ hrough 767 and (name N or name CA or name C or name O or name CB )) or resid 768 \ through 776 or resid 782 through 785 or (resid 786 through 788 and (name N or n \ ame CA or name C or name O or name CB )) or resid 789 through 801 or resid 803 t \ hrough 814 or (resid 815 and (name N or name CA or name C or name O or name CB ) \ ) or resid 816 through 819 or resid 901)) } ncs_group { reference = (chain 'F' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 through 96 or (resid 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 101 or (resid 102 through 103 and (name N or n \ ame CA or name C or name O or name CB )) or resid 104 through 126 or (resid 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 through 17 \ 0 or resid 172 through 208)) selection = (chain 'H' and (resid 6 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 81 or resid 93 through 106 or (resi \ d 107 and (name N or name CA or name C or name O or name CB )) or resid 108 thro \ ugh 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) o \ r resid 118 through 165 or (resid 166 through 171 and (name N or name CA or name \ C or name O or name CB )) or resid 172 through 179 or (resid 180 and (name N or \ name CA or name C or name O or name CB )) or resid 181 through 208)) } 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: 2.130 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.200 Find NCS groups from input model: 0.730 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 : 0.003 0.091 13985 Z= 0.170 Angle : 0.855 12.754 19093 Z= 0.432 Chirality : 0.048 0.290 2243 Planarity : 0.005 0.079 2354 Dihedral : 12.704 87.055 4662 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.29 (0.19), residues: 1833 helix: 0.19 (0.16), residues: 996 sheet: -0.50 (0.59), residues: 88 loop : -2.39 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 602 HIS 0.007 0.001 HIS H 199 PHE 0.059 0.002 PHE F 141 TYR 0.014 0.001 TYR A 436 ARG 0.005 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.13348 ( 779) hydrogen bonds : angle 6.04889 ( 2307) SS BOND : bond 0.00090 ( 8) SS BOND : angle 1.65674 ( 16) covalent geometry : bond 0.00350 (13975) covalent geometry : angle 0.85446 (19077) Misc. bond : bond 0.00686 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 192 MET cc_start: 0.7316 (ppp) cc_final: 0.6843 (ppp) REVERT: F 207 GLN cc_start: 0.6994 (mp10) cc_final: 0.6552 (mp10) REVERT: A 434 TYR cc_start: 0.8281 (p90) cc_final: 0.7521 (p90) REVERT: A 499 MET cc_start: 0.7385 (pmm) cc_final: 0.6606 (pmm) REVERT: A 524 CYS cc_start: 0.8923 (m) cc_final: 0.8238 (m) REVERT: A 625 MET cc_start: 0.8278 (pmm) cc_final: 0.7485 (pmm) REVERT: B 530 CYS cc_start: 0.8539 (t) cc_final: 0.8275 (t) REVERT: B 612 LEU cc_start: 0.9191 (pp) cc_final: 0.8967 (pp) REVERT: B 772 LYS cc_start: 0.6934 (pttt) cc_final: 0.6704 (pttt) REVERT: B 791 LEU cc_start: 0.8612 (tp) cc_final: 0.8333 (tp) REVERT: C 400 PRO cc_start: 0.8720 (Cg_endo) cc_final: 0.8506 (Cg_exo) REVERT: C 434 TYR cc_start: 0.8207 (p90) cc_final: 0.7228 (p90) REVERT: C 479 LEU cc_start: 0.8586 (pt) cc_final: 0.8346 (mm) REVERT: C 756 ASP cc_start: 0.8226 (m-30) cc_final: 0.7873 (m-30) REVERT: C 761 LYS cc_start: 0.7832 (pptt) cc_final: 0.7127 (pttm) REVERT: D 505 MET cc_start: 0.7506 (ppp) cc_final: 0.7178 (ptm) REVERT: D 530 CYS cc_start: 0.9154 (m) cc_final: 0.8820 (m) REVERT: D 622 LEU cc_start: 0.9265 (tp) cc_final: 0.8966 (tp) REVERT: D 626 LEU cc_start: 0.9295 (mm) cc_final: 0.9085 (mp) REVERT: D 770 TYR cc_start: 0.7673 (m-80) cc_final: 0.7437 (m-10) REVERT: D 771 ASP cc_start: 0.7684 (m-30) cc_final: 0.7262 (m-30) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2259 time to fit residues: 112.9607 Evaluate side-chains 260 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 0.0570 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 132 HIS ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098677 restraints weight = 48216.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.098686 restraints weight = 40000.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099552 restraints weight = 30976.103| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13985 Z= 0.147 Angle : 0.605 8.839 19093 Z= 0.307 Chirality : 0.039 0.188 2243 Planarity : 0.004 0.069 2354 Dihedral : 4.695 65.519 2068 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1833 helix: 1.24 (0.17), residues: 1009 sheet: -0.27 (0.65), residues: 71 loop : -2.24 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 762 HIS 0.005 0.001 HIS F 132 PHE 0.035 0.001 PHE H 182 TYR 0.013 0.001 TYR B 770 ARG 0.005 0.001 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 779) hydrogen bonds : angle 4.39245 ( 2307) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.80603 ( 16) covalent geometry : bond 0.00321 (13975) covalent geometry : angle 0.60466 (19077) Misc. bond : bond 0.00588 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 PHE cc_start: 0.7849 (m-80) cc_final: 0.7534 (m-80) REVERT: F 192 MET cc_start: 0.7973 (ppp) cc_final: 0.7618 (ppp) REVERT: H 192 MET cc_start: 0.7601 (ppp) cc_final: 0.7375 (ppp) REVERT: A 402 VAL cc_start: 0.7191 (t) cc_final: 0.6887 (t) REVERT: A 500 ILE cc_start: 0.9022 (tp) cc_final: 0.8813 (tp) REVERT: A 524 CYS cc_start: 0.9005 (m) cc_final: 0.8502 (m) REVERT: A 605 THR cc_start: 0.9213 (p) cc_final: 0.8698 (t) REVERT: B 631 MET cc_start: 0.6163 (tpp) cc_final: 0.5944 (tpp) REVERT: B 772 LYS cc_start: 0.6701 (pttt) cc_final: 0.5904 (pttt) REVERT: B 791 LEU cc_start: 0.8950 (tp) cc_final: 0.8523 (tp) REVERT: C 399 ASP cc_start: 0.7752 (t0) cc_final: 0.7507 (t70) REVERT: C 400 PRO cc_start: 0.8875 (Cg_endo) cc_final: 0.8556 (Cg_exo) REVERT: C 479 LEU cc_start: 0.8732 (pt) cc_final: 0.8385 (mm) REVERT: D 529 MET cc_start: 0.7733 (pmm) cc_final: 0.7194 (pmm) REVERT: D 530 CYS cc_start: 0.9230 (m) cc_final: 0.8896 (m) REVERT: D 606 VAL cc_start: 0.9720 (m) cc_final: 0.9477 (p) REVERT: D 613 ILE cc_start: 0.8928 (mm) cc_final: 0.8676 (mm) REVERT: D 716 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7717 (tp-100) REVERT: D 770 TYR cc_start: 0.8113 (m-80) cc_final: 0.7163 (m-10) REVERT: D 771 ASP cc_start: 0.8094 (m-30) cc_final: 0.7814 (m-30) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.2161 time to fit residues: 100.7424 Evaluate side-chains 232 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.115777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.092394 restraints weight = 49861.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091218 restraints weight = 44315.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092065 restraints weight = 42122.069| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13985 Z= 0.230 Angle : 0.698 8.756 19093 Z= 0.364 Chirality : 0.042 0.174 2243 Planarity : 0.005 0.063 2354 Dihedral : 5.115 56.677 2068 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.23 % Allowed : 6.37 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.31 (0.20), residues: 1833 helix: 1.26 (0.16), residues: 1016 sheet: -0.16 (0.62), residues: 77 loop : -2.44 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 762 HIS 0.005 0.001 HIS F 132 PHE 0.026 0.002 PHE C 619 TYR 0.022 0.002 TYR B 770 ARG 0.009 0.001 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 779) hydrogen bonds : angle 4.56496 ( 2307) SS BOND : bond 0.00442 ( 8) SS BOND : angle 0.91665 ( 16) covalent geometry : bond 0.00500 (13975) covalent geometry : angle 0.69790 (19077) Misc. bond : bond 0.00765 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.7417 (tpt) cc_final: 0.7173 (tpt) REVERT: F 99 ARG cc_start: 0.7889 (tpm170) cc_final: 0.7263 (tpm170) REVERT: F 182 PHE cc_start: 0.7943 (m-80) cc_final: 0.7575 (m-80) REVERT: F 192 MET cc_start: 0.8212 (ppp) cc_final: 0.7878 (ppp) REVERT: H 174 TYR cc_start: 0.7363 (m-80) cc_final: 0.6342 (p90) REVERT: A 487 PHE cc_start: 0.7621 (m-80) cc_final: 0.7358 (m-80) REVERT: A 523 MET cc_start: 0.8535 (tmm) cc_final: 0.8287 (tmm) REVERT: A 524 CYS cc_start: 0.9250 (m) cc_final: 0.8818 (m) REVERT: A 605 THR cc_start: 0.9172 (p) cc_final: 0.8675 (t) REVERT: A 625 MET cc_start: 0.8286 (pmm) cc_final: 0.7861 (pmm) REVERT: A 676 SER cc_start: 0.7741 (m) cc_final: 0.7456 (t) REVERT: B 631 MET cc_start: 0.7334 (tpp) cc_final: 0.6800 (tpp) REVERT: B 710 MET cc_start: 0.8712 (tpt) cc_final: 0.7618 (tpp) REVERT: B 772 LYS cc_start: 0.6849 (pttt) cc_final: 0.5912 (pttt) REVERT: B 791 LEU cc_start: 0.9253 (tp) cc_final: 0.8815 (tp) REVERT: C 459 MET cc_start: 0.8459 (mpp) cc_final: 0.7761 (mtt) REVERT: C 489 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8777 (mmtm) REVERT: C 515 ASP cc_start: 0.9163 (t0) cc_final: 0.8868 (t0) REVERT: C 634 ASP cc_start: 0.8777 (t0) cc_final: 0.8543 (t0) REVERT: C 717 MET cc_start: 0.8365 (pmm) cc_final: 0.8129 (pmm) REVERT: C 757 LYS cc_start: 0.9022 (mttt) cc_final: 0.8623 (mtpp) REVERT: D 529 MET cc_start: 0.7699 (pmm) cc_final: 0.7013 (pmm) REVERT: D 606 VAL cc_start: 0.9730 (m) cc_final: 0.9444 (p) REVERT: D 613 ILE cc_start: 0.9661 (mm) cc_final: 0.9151 (tp) REVERT: D 672 MET cc_start: 0.8746 (tmm) cc_final: 0.8397 (tpt) REVERT: D 710 MET cc_start: 0.8073 (mpp) cc_final: 0.7849 (mpp) REVERT: D 716 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8142 (tp-100) REVERT: D 771 ASP cc_start: 0.8478 (m-30) cc_final: 0.8246 (m-30) outliers start: 3 outliers final: 2 residues processed: 285 average time/residue: 0.2307 time to fit residues: 102.9327 Evaluate side-chains 224 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 156 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 173 optimal weight: 0.0020 chunk 138 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS A 431 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095863 restraints weight = 48241.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095352 restraints weight = 46753.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.096326 restraints weight = 38085.266| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13985 Z= 0.119 Angle : 0.594 8.092 19093 Z= 0.301 Chirality : 0.040 0.152 2243 Planarity : 0.004 0.073 2354 Dihedral : 4.820 57.142 2068 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.15 % Allowed : 3.49 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.13 (0.20), residues: 1833 helix: 1.71 (0.17), residues: 1000 sheet: -0.27 (0.63), residues: 82 loop : -2.26 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 608 HIS 0.007 0.001 HIS F 199 PHE 0.023 0.001 PHE F 141 TYR 0.014 0.001 TYR D 649 ARG 0.004 0.000 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 779) hydrogen bonds : angle 4.18899 ( 2307) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.09387 ( 16) covalent geometry : bond 0.00264 (13975) covalent geometry : angle 0.59379 (19077) Misc. bond : bond 0.00670 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.7823 (tpm170) cc_final: 0.7275 (tpm170) REVERT: F 130 THR cc_start: 0.8182 (t) cc_final: 0.7862 (p) REVERT: F 156 TYR cc_start: 0.7474 (m-10) cc_final: 0.7199 (m-80) REVERT: F 182 PHE cc_start: 0.8088 (m-80) cc_final: 0.7681 (m-80) REVERT: F 192 MET cc_start: 0.8084 (ppp) cc_final: 0.7748 (ppp) REVERT: H 192 MET cc_start: 0.7537 (ppp) cc_final: 0.7024 (ppp) REVERT: A 397 LEU cc_start: 0.7282 (pt) cc_final: 0.6959 (pt) REVERT: A 420 TYR cc_start: 0.8286 (t80) cc_final: 0.7952 (t80) REVERT: A 434 TYR cc_start: 0.8150 (p90) cc_final: 0.7883 (p90) REVERT: A 487 PHE cc_start: 0.7573 (m-80) cc_final: 0.7278 (m-80) REVERT: A 523 MET cc_start: 0.8498 (tmm) cc_final: 0.8189 (tmm) REVERT: A 524 CYS cc_start: 0.8794 (m) cc_final: 0.8339 (m) REVERT: A 605 THR cc_start: 0.8925 (p) cc_final: 0.8357 (t) REVERT: A 625 MET cc_start: 0.8539 (pmm) cc_final: 0.8145 (pmm) REVERT: A 676 SER cc_start: 0.7694 (m) cc_final: 0.7438 (t) REVERT: A 703 THR cc_start: 0.8710 (p) cc_final: 0.8405 (p) REVERT: B 530 CYS cc_start: 0.8496 (t) cc_final: 0.8286 (t) REVERT: B 622 LEU cc_start: 0.9598 (tp) cc_final: 0.9225 (tp) REVERT: B 631 MET cc_start: 0.7324 (tpp) cc_final: 0.6660 (tpp) REVERT: B 710 MET cc_start: 0.8674 (tpt) cc_final: 0.7534 (tpp) REVERT: B 772 LYS cc_start: 0.6717 (pttt) cc_final: 0.6215 (pttt) REVERT: B 791 LEU cc_start: 0.9184 (tp) cc_final: 0.8690 (tp) REVERT: C 399 ASP cc_start: 0.7619 (t70) cc_final: 0.7104 (t0) REVERT: C 515 ASP cc_start: 0.8926 (t0) cc_final: 0.8639 (t70) REVERT: C 634 ASP cc_start: 0.8523 (t0) cc_final: 0.8314 (t0) REVERT: C 756 ASP cc_start: 0.8349 (m-30) cc_final: 0.8135 (m-30) REVERT: D 606 VAL cc_start: 0.9711 (m) cc_final: 0.9458 (p) REVERT: D 622 LEU cc_start: 0.9434 (tp) cc_final: 0.9223 (tp) REVERT: D 672 MET cc_start: 0.8624 (tmm) cc_final: 0.8335 (tpt) REVERT: D 716 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8441 (tp-100) REVERT: D 771 ASP cc_start: 0.8311 (m-30) cc_final: 0.8093 (m-30) outliers start: 2 outliers final: 0 residues processed: 300 average time/residue: 0.2176 time to fit residues: 100.2740 Evaluate side-chains 244 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 134 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS D 793 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.114306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089843 restraints weight = 49628.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088936 restraints weight = 40285.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089354 restraints weight = 34289.674| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13985 Z= 0.210 Angle : 0.675 9.554 19093 Z= 0.350 Chirality : 0.042 0.176 2243 Planarity : 0.004 0.078 2354 Dihedral : 5.121 59.026 2068 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.89 % Rotamer: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.20), residues: 1833 helix: 1.56 (0.16), residues: 1015 sheet: -1.13 (0.54), residues: 99 loop : -2.39 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 768 HIS 0.007 0.001 HIS F 199 PHE 0.047 0.002 PHE H 182 TYR 0.026 0.002 TYR C 446 ARG 0.007 0.001 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 779) hydrogen bonds : angle 4.39885 ( 2307) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.06940 ( 16) covalent geometry : bond 0.00462 (13975) covalent geometry : angle 0.67467 (19077) Misc. bond : bond 0.00756 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.7349 (tpm170) cc_final: 0.6846 (tpm170) REVERT: F 156 TYR cc_start: 0.8101 (m-10) cc_final: 0.7762 (m-80) REVERT: F 182 PHE cc_start: 0.8322 (m-80) cc_final: 0.7775 (m-80) REVERT: F 192 MET cc_start: 0.8257 (ppp) cc_final: 0.7913 (ppp) REVERT: H 192 MET cc_start: 0.7390 (ppp) cc_final: 0.6995 (ppp) REVERT: A 420 TYR cc_start: 0.8592 (t80) cc_final: 0.8323 (t80) REVERT: A 492 MET cc_start: 0.8852 (ptm) cc_final: 0.8381 (ptp) REVERT: A 523 MET cc_start: 0.8538 (tmm) cc_final: 0.8309 (tmm) REVERT: A 524 CYS cc_start: 0.8915 (m) cc_final: 0.8469 (m) REVERT: A 605 THR cc_start: 0.8978 (p) cc_final: 0.8434 (t) REVERT: A 634 ASP cc_start: 0.8736 (t0) cc_final: 0.8529 (t0) REVERT: A 676 SER cc_start: 0.7702 (m) cc_final: 0.7430 (t) REVERT: A 703 THR cc_start: 0.8636 (p) cc_final: 0.8238 (p) REVERT: B 530 CYS cc_start: 0.8727 (t) cc_final: 0.8474 (t) REVERT: B 622 LEU cc_start: 0.9642 (tp) cc_final: 0.9410 (tp) REVERT: B 710 MET cc_start: 0.8773 (tpt) cc_final: 0.7584 (tpp) REVERT: B 772 LYS cc_start: 0.6918 (pttt) cc_final: 0.6126 (pttt) REVERT: B 791 LEU cc_start: 0.9228 (tp) cc_final: 0.8696 (tp) REVERT: C 399 ASP cc_start: 0.7815 (t70) cc_final: 0.7341 (t0) REVERT: C 525 ILE cc_start: 0.9400 (tp) cc_final: 0.9130 (tp) REVERT: C 634 ASP cc_start: 0.8804 (t0) cc_final: 0.8447 (t0) REVERT: C 756 ASP cc_start: 0.8522 (m-30) cc_final: 0.8309 (m-30) REVERT: D 529 MET cc_start: 0.7761 (pmm) cc_final: 0.7357 (pmm) REVERT: D 606 VAL cc_start: 0.9698 (m) cc_final: 0.9429 (p) REVERT: D 613 ILE cc_start: 0.9647 (mm) cc_final: 0.9251 (tp) REVERT: D 672 MET cc_start: 0.8795 (tmm) cc_final: 0.8467 (tpt) REVERT: D 716 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8085 (tp-100) REVERT: D 798 PHE cc_start: 0.8102 (m-10) cc_final: 0.7716 (m-10) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.2056 time to fit residues: 85.4205 Evaluate side-chains 220 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 85 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 0.0980 chunk 158 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094103 restraints weight = 49336.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093916 restraints weight = 44347.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094802 restraints weight = 38627.274| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13985 Z= 0.126 Angle : 0.626 9.008 19093 Z= 0.316 Chirality : 0.041 0.208 2243 Planarity : 0.004 0.059 2354 Dihedral : 4.924 57.975 2068 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.18 (0.20), residues: 1833 helix: 1.76 (0.16), residues: 1013 sheet: -0.76 (0.51), residues: 114 loop : -2.32 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 768 HIS 0.007 0.001 HIS F 199 PHE 0.042 0.002 PHE H 182 TYR 0.014 0.001 TYR C 446 ARG 0.005 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 779) hydrogen bonds : angle 4.21492 ( 2307) SS BOND : bond 0.00220 ( 8) SS BOND : angle 0.88792 ( 16) covalent geometry : bond 0.00283 (13975) covalent geometry : angle 0.62605 (19077) Misc. bond : bond 0.00698 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.6944 (tpm170) cc_final: 0.6601 (tpm170) REVERT: F 130 THR cc_start: 0.7670 (t) cc_final: 0.7210 (p) REVERT: F 182 PHE cc_start: 0.8280 (m-80) cc_final: 0.7732 (m-80) REVERT: F 192 MET cc_start: 0.7953 (ppp) cc_final: 0.7570 (ppp) REVERT: H 192 MET cc_start: 0.7179 (ppp) cc_final: 0.6869 (ppp) REVERT: A 420 TYR cc_start: 0.8101 (t80) cc_final: 0.7891 (t80) REVERT: A 434 TYR cc_start: 0.8058 (p90) cc_final: 0.7630 (p90) REVERT: A 523 MET cc_start: 0.8454 (tmm) cc_final: 0.8156 (tmm) REVERT: A 524 CYS cc_start: 0.8871 (m) cc_final: 0.8419 (m) REVERT: A 539 VAL cc_start: 0.8039 (t) cc_final: 0.7793 (p) REVERT: A 605 THR cc_start: 0.8964 (p) cc_final: 0.8419 (t) REVERT: A 625 MET cc_start: 0.8507 (pmm) cc_final: 0.7819 (pmm) REVERT: A 676 SER cc_start: 0.7649 (m) cc_final: 0.7433 (t) REVERT: A 703 THR cc_start: 0.8517 (p) cc_final: 0.8092 (p) REVERT: B 530 CYS cc_start: 0.8513 (t) cc_final: 0.8288 (t) REVERT: B 613 ILE cc_start: 0.9380 (tp) cc_final: 0.9143 (tt) REVERT: B 622 LEU cc_start: 0.9341 (tp) cc_final: 0.9003 (tp) REVERT: B 631 MET cc_start: 0.7049 (tpp) cc_final: 0.6714 (tpp) REVERT: B 710 MET cc_start: 0.8693 (tpt) cc_final: 0.7744 (tpp) REVERT: B 772 LYS cc_start: 0.6977 (pttt) cc_final: 0.5981 (pttt) REVERT: B 791 LEU cc_start: 0.9224 (tp) cc_final: 0.8792 (tp) REVERT: C 399 ASP cc_start: 0.7506 (t70) cc_final: 0.6979 (t0) REVERT: C 515 ASP cc_start: 0.9250 (t70) cc_final: 0.9035 (t70) REVERT: C 524 CYS cc_start: 0.8518 (p) cc_final: 0.7412 (t) REVERT: C 525 ILE cc_start: 0.9289 (tp) cc_final: 0.8844 (tp) REVERT: C 606 LEU cc_start: 0.8290 (tp) cc_final: 0.8030 (tp) REVERT: C 634 ASP cc_start: 0.8600 (t0) cc_final: 0.8365 (t0) REVERT: D 403 MET cc_start: 0.8623 (tpt) cc_final: 0.7903 (tpp) REVERT: D 529 MET cc_start: 0.7767 (pmm) cc_final: 0.7178 (pmm) REVERT: D 606 VAL cc_start: 0.9683 (m) cc_final: 0.9405 (p) REVERT: D 613 ILE cc_start: 0.9623 (mm) cc_final: 0.9320 (tp) REVERT: D 672 MET cc_start: 0.8587 (tmm) cc_final: 0.8364 (tpt) REVERT: D 716 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8411 (tp-100) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.2176 time to fit residues: 91.2001 Evaluate side-chains 224 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 174 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 97 optimal weight: 0.0010 chunk 173 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 170 optimal weight: 0.2980 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN C 410 GLN ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097393 restraints weight = 48868.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.096846 restraints weight = 48282.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098123 restraints weight = 38592.335| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 13985 Z= 0.114 Angle : 0.628 7.611 19093 Z= 0.313 Chirality : 0.040 0.214 2243 Planarity : 0.004 0.050 2354 Dihedral : 4.772 56.601 2068 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.86 % Favored : 95.09 % Rotamer: Outliers : 0.15 % Allowed : 2.05 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.20), residues: 1833 helix: 1.85 (0.17), residues: 1011 sheet: -1.05 (0.47), residues: 129 loop : -2.19 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 602 HIS 0.010 0.001 HIS F 199 PHE 0.039 0.001 PHE H 182 TYR 0.013 0.001 TYR H 156 ARG 0.003 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 779) hydrogen bonds : angle 4.14536 ( 2307) SS BOND : bond 0.00186 ( 8) SS BOND : angle 0.83276 ( 16) covalent geometry : bond 0.00251 (13975) covalent geometry : angle 0.62774 (19077) Misc. bond : bond 0.00611 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.6890 (tpm170) cc_final: 0.6621 (tpm170) REVERT: F 182 PHE cc_start: 0.8249 (m-80) cc_final: 0.7699 (m-80) REVERT: F 192 MET cc_start: 0.8136 (ppp) cc_final: 0.7784 (ppp) REVERT: H 34 LEU cc_start: 0.7798 (mm) cc_final: 0.7586 (mm) REVERT: H 78 LYS cc_start: 0.7780 (mttp) cc_final: 0.7561 (mtmt) REVERT: A 434 TYR cc_start: 0.8005 (p90) cc_final: 0.7676 (p90) REVERT: A 523 MET cc_start: 0.8508 (tmm) cc_final: 0.8239 (tmm) REVERT: A 524 CYS cc_start: 0.8764 (m) cc_final: 0.8284 (m) REVERT: A 605 THR cc_start: 0.8866 (p) cc_final: 0.8282 (t) REVERT: A 676 SER cc_start: 0.7681 (m) cc_final: 0.7467 (t) REVERT: A 703 THR cc_start: 0.8176 (p) cc_final: 0.7858 (p) REVERT: B 613 ILE cc_start: 0.9338 (tp) cc_final: 0.9046 (tt) REVERT: B 622 LEU cc_start: 0.9397 (tp) cc_final: 0.8924 (tp) REVERT: B 631 MET cc_start: 0.7231 (tpp) cc_final: 0.6477 (tpp) REVERT: B 710 MET cc_start: 0.8519 (tpt) cc_final: 0.7708 (tpp) REVERT: B 772 LYS cc_start: 0.7271 (pttt) cc_final: 0.6757 (pttt) REVERT: B 791 LEU cc_start: 0.9241 (tp) cc_final: 0.8877 (tp) REVERT: C 399 ASP cc_start: 0.7839 (t70) cc_final: 0.7238 (t0) REVERT: C 525 ILE cc_start: 0.9121 (tp) cc_final: 0.8631 (tp) REVERT: C 606 LEU cc_start: 0.8198 (tp) cc_final: 0.7617 (tp) REVERT: C 634 ASP cc_start: 0.8478 (t0) cc_final: 0.8215 (t0) REVERT: C 703 THR cc_start: 0.9083 (m) cc_final: 0.8856 (m) REVERT: C 756 ASP cc_start: 0.8146 (m-30) cc_final: 0.7913 (m-30) REVERT: C 759 LYS cc_start: 0.9048 (tttp) cc_final: 0.8579 (tptm) REVERT: D 403 MET cc_start: 0.8457 (tpt) cc_final: 0.7731 (tpp) REVERT: D 529 MET cc_start: 0.7644 (pmm) cc_final: 0.7106 (pmm) REVERT: D 606 VAL cc_start: 0.9658 (m) cc_final: 0.9392 (p) REVERT: D 613 ILE cc_start: 0.9515 (mm) cc_final: 0.9146 (tp) REVERT: D 622 LEU cc_start: 0.9555 (tp) cc_final: 0.9263 (tp) REVERT: D 716 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8063 (tp-100) REVERT: D 770 TYR cc_start: 0.8364 (m-10) cc_final: 0.7898 (m-10) outliers start: 2 outliers final: 0 residues processed: 285 average time/residue: 0.2090 time to fit residues: 91.6045 Evaluate side-chains 225 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.0000 chunk 22 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 175 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS H 199 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.116734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093384 restraints weight = 49877.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093276 restraints weight = 44241.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093966 restraints weight = 39246.441| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13985 Z= 0.170 Angle : 0.668 9.723 19093 Z= 0.339 Chirality : 0.041 0.207 2243 Planarity : 0.004 0.079 2354 Dihedral : 4.968 58.230 2068 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.23 (0.20), residues: 1833 helix: 1.80 (0.16), residues: 1015 sheet: -0.83 (0.56), residues: 86 loop : -2.23 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 64 HIS 0.009 0.001 HIS F 199 PHE 0.041 0.002 PHE H 182 TYR 0.022 0.001 TYR A 698 ARG 0.009 0.001 ARG H 65 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 779) hydrogen bonds : angle 4.26046 ( 2307) SS BOND : bond 0.00282 ( 8) SS BOND : angle 0.78146 ( 16) covalent geometry : bond 0.00380 (13975) covalent geometry : angle 0.66836 (19077) Misc. bond : bond 0.00726 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.7468 (tpt) cc_final: 0.7103 (tpt) REVERT: F 99 ARG cc_start: 0.7092 (tpm170) cc_final: 0.6667 (tpm170) REVERT: F 156 TYR cc_start: 0.7992 (m-10) cc_final: 0.7620 (m-10) REVERT: F 182 PHE cc_start: 0.8430 (m-80) cc_final: 0.7760 (m-80) REVERT: F 192 MET cc_start: 0.8189 (ppp) cc_final: 0.7943 (ppp) REVERT: A 434 TYR cc_start: 0.7974 (p90) cc_final: 0.7738 (p90) REVERT: A 523 MET cc_start: 0.8512 (tmm) cc_final: 0.8218 (tmm) REVERT: A 524 CYS cc_start: 0.8911 (m) cc_final: 0.8501 (m) REVERT: A 605 THR cc_start: 0.9099 (p) cc_final: 0.8649 (t) REVERT: A 619 PHE cc_start: 0.8216 (m-10) cc_final: 0.7973 (m-80) REVERT: A 625 MET cc_start: 0.8457 (pmm) cc_final: 0.7413 (pmm) REVERT: A 703 THR cc_start: 0.8600 (p) cc_final: 0.8312 (p) REVERT: B 613 ILE cc_start: 0.9356 (tp) cc_final: 0.9099 (tt) REVERT: B 631 MET cc_start: 0.7223 (tpp) cc_final: 0.6784 (tpp) REVERT: B 710 MET cc_start: 0.8627 (tpt) cc_final: 0.7466 (tpp) REVERT: B 772 LYS cc_start: 0.7741 (pttt) cc_final: 0.6949 (pttt) REVERT: B 791 LEU cc_start: 0.9244 (tp) cc_final: 0.8856 (tp) REVERT: C 399 ASP cc_start: 0.7529 (t70) cc_final: 0.7051 (t0) REVERT: C 515 ASP cc_start: 0.9041 (t70) cc_final: 0.8739 (t70) REVERT: C 525 ILE cc_start: 0.9196 (tp) cc_final: 0.8809 (tp) REVERT: C 606 LEU cc_start: 0.8799 (tp) cc_final: 0.8184 (tp) REVERT: C 634 ASP cc_start: 0.8655 (t0) cc_final: 0.8395 (t0) REVERT: C 703 THR cc_start: 0.9085 (m) cc_final: 0.8843 (m) REVERT: D 403 MET cc_start: 0.8882 (tpt) cc_final: 0.8092 (tpp) REVERT: D 606 VAL cc_start: 0.9694 (m) cc_final: 0.9445 (p) REVERT: D 613 ILE cc_start: 0.9579 (mm) cc_final: 0.9147 (tp) REVERT: D 716 GLN cc_start: 0.8897 (mm-40) cc_final: 0.7960 (tp-100) REVERT: D 770 TYR cc_start: 0.8465 (m-10) cc_final: 0.7958 (m-10) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.2073 time to fit residues: 87.7055 Evaluate side-chains 223 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 86 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.0030 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS H 199 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.095469 restraints weight = 49357.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095481 restraints weight = 41830.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096050 restraints weight = 39325.119| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13985 Z= 0.128 Angle : 0.649 10.262 19093 Z= 0.325 Chirality : 0.041 0.218 2243 Planarity : 0.004 0.067 2354 Dihedral : 4.868 57.351 2068 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.20), residues: 1833 helix: 1.84 (0.17), residues: 1016 sheet: -0.44 (0.59), residues: 75 loop : -2.23 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 602 HIS 0.007 0.001 HIS F 199 PHE 0.039 0.002 PHE H 182 TYR 0.018 0.001 TYR H 174 ARG 0.005 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 779) hydrogen bonds : angle 4.17830 ( 2307) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.72465 ( 16) covalent geometry : bond 0.00290 (13975) covalent geometry : angle 0.64876 (19077) Misc. bond : bond 0.00675 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.6938 (tpm170) cc_final: 0.6650 (tpm170) REVERT: F 156 TYR cc_start: 0.7775 (m-10) cc_final: 0.7529 (m-10) REVERT: F 182 PHE cc_start: 0.8424 (m-80) cc_final: 0.7749 (m-80) REVERT: A 434 TYR cc_start: 0.8249 (p90) cc_final: 0.8004 (p90) REVERT: A 523 MET cc_start: 0.8503 (tmm) cc_final: 0.8278 (tmm) REVERT: A 524 CYS cc_start: 0.8862 (m) cc_final: 0.8388 (m) REVERT: A 605 THR cc_start: 0.8976 (p) cc_final: 0.8447 (t) REVERT: A 625 MET cc_start: 0.8431 (pmm) cc_final: 0.7625 (pmm) REVERT: A 703 THR cc_start: 0.8551 (p) cc_final: 0.8229 (p) REVERT: B 631 MET cc_start: 0.7351 (tpp) cc_final: 0.6779 (tpp) REVERT: B 710 MET cc_start: 0.8556 (tpt) cc_final: 0.7372 (tpp) REVERT: B 740 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8782 (mmmt) REVERT: B 772 LYS cc_start: 0.7509 (pttt) cc_final: 0.6630 (pttt) REVERT: B 791 LEU cc_start: 0.9224 (tp) cc_final: 0.8831 (tp) REVERT: C 399 ASP cc_start: 0.7439 (t70) cc_final: 0.6974 (t0) REVERT: C 515 ASP cc_start: 0.9070 (t70) cc_final: 0.8832 (t70) REVERT: C 525 ILE cc_start: 0.9144 (tp) cc_final: 0.8751 (tp) REVERT: C 606 LEU cc_start: 0.8701 (tp) cc_final: 0.8092 (tp) REVERT: C 634 ASP cc_start: 0.8565 (t0) cc_final: 0.8299 (t0) REVERT: C 756 ASP cc_start: 0.8487 (m-30) cc_final: 0.8227 (m-30) REVERT: C 759 LYS cc_start: 0.9134 (tttp) cc_final: 0.8641 (tptm) REVERT: D 403 MET cc_start: 0.8801 (tpt) cc_final: 0.8054 (tpp) REVERT: D 529 MET cc_start: 0.7832 (pmm) cc_final: 0.7501 (pmm) REVERT: D 606 VAL cc_start: 0.9673 (m) cc_final: 0.9416 (p) REVERT: D 613 ILE cc_start: 0.9501 (mm) cc_final: 0.9151 (tp) REVERT: D 716 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8221 (tp-100) REVERT: D 770 TYR cc_start: 0.8349 (m-10) cc_final: 0.7832 (m-10) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2097 time to fit residues: 87.8705 Evaluate side-chains 228 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 61 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 157 optimal weight: 0.0270 chunk 152 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 HIS H 60 HIS H 199 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.119043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.096084 restraints weight = 49258.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095235 restraints weight = 44557.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096170 restraints weight = 40042.930| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 13985 Z= 0.125 Angle : 0.661 10.069 19093 Z= 0.330 Chirality : 0.041 0.224 2243 Planarity : 0.004 0.061 2354 Dihedral : 4.857 57.184 2068 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.22 (0.20), residues: 1833 helix: 1.77 (0.16), residues: 1016 sheet: -0.81 (0.54), residues: 92 loop : -2.23 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 602 HIS 0.009 0.001 HIS F 199 PHE 0.038 0.002 PHE H 182 TYR 0.017 0.001 TYR H 174 ARG 0.005 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 779) hydrogen bonds : angle 4.19577 ( 2307) SS BOND : bond 0.00217 ( 8) SS BOND : angle 0.73587 ( 16) covalent geometry : bond 0.00285 (13975) covalent geometry : angle 0.66086 (19077) Misc. bond : bond 0.00659 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.6987 (tpm170) cc_final: 0.6608 (tpm170) REVERT: F 142 PHE cc_start: 0.7883 (m-80) cc_final: 0.7452 (m-80) REVERT: F 156 TYR cc_start: 0.7799 (m-10) cc_final: 0.7533 (m-10) REVERT: F 176 TYR cc_start: 0.6909 (m-80) cc_final: 0.6661 (m-80) REVERT: F 182 PHE cc_start: 0.8428 (m-80) cc_final: 0.7759 (m-80) REVERT: H 187 PHE cc_start: 0.8657 (t80) cc_final: 0.8090 (t80) REVERT: A 434 TYR cc_start: 0.8191 (p90) cc_final: 0.7954 (p90) REVERT: A 523 MET cc_start: 0.8472 (tmm) cc_final: 0.8151 (tmm) REVERT: A 524 CYS cc_start: 0.8887 (m) cc_final: 0.8471 (m) REVERT: A 605 THR cc_start: 0.8961 (p) cc_final: 0.8400 (t) REVERT: A 625 MET cc_start: 0.8376 (pmm) cc_final: 0.7613 (pmm) REVERT: B 622 LEU cc_start: 0.9376 (tp) cc_final: 0.8914 (tp) REVERT: B 710 MET cc_start: 0.8426 (tpt) cc_final: 0.7341 (tpp) REVERT: B 740 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8772 (mmmt) REVERT: B 772 LYS cc_start: 0.7603 (pttt) cc_final: 0.6764 (pttt) REVERT: B 791 LEU cc_start: 0.9238 (tp) cc_final: 0.8767 (tp) REVERT: C 399 ASP cc_start: 0.7759 (t70) cc_final: 0.7132 (t0) REVERT: C 525 ILE cc_start: 0.9111 (tp) cc_final: 0.8721 (tp) REVERT: C 606 LEU cc_start: 0.8735 (tp) cc_final: 0.8056 (tp) REVERT: C 634 ASP cc_start: 0.8524 (t0) cc_final: 0.8270 (t0) REVERT: C 703 THR cc_start: 0.9088 (m) cc_final: 0.8863 (m) REVERT: C 756 ASP cc_start: 0.8159 (m-30) cc_final: 0.7933 (m-30) REVERT: D 402 ILE cc_start: 0.8440 (tp) cc_final: 0.8144 (tp) REVERT: D 403 MET cc_start: 0.8748 (tpt) cc_final: 0.8022 (tpp) REVERT: D 529 MET cc_start: 0.7778 (pmm) cc_final: 0.7421 (pmm) REVERT: D 606 VAL cc_start: 0.9651 (m) cc_final: 0.9400 (p) REVERT: D 613 ILE cc_start: 0.9501 (mm) cc_final: 0.9019 (tp) REVERT: D 622 LEU cc_start: 0.9384 (tp) cc_final: 0.8935 (tp) REVERT: D 716 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8239 (tp-100) REVERT: D 770 TYR cc_start: 0.8420 (m-10) cc_final: 0.7943 (m-10) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2068 time to fit residues: 85.5778 Evaluate side-chains 226 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 38 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 78 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 HIS ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.097915 restraints weight = 50157.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.096716 restraints weight = 46722.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.097849 restraints weight = 41470.266| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 13985 Z= 0.117 Angle : 0.659 10.591 19093 Z= 0.326 Chirality : 0.041 0.232 2243 Planarity : 0.004 0.054 2354 Dihedral : 4.772 56.241 2068 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.31 (0.20), residues: 1833 helix: 1.82 (0.17), residues: 1017 sheet: -0.58 (0.50), residues: 110 loop : -2.22 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 602 HIS 0.002 0.000 HIS H 199 PHE 0.037 0.002 PHE H 182 TYR 0.017 0.001 TYR B 407 ARG 0.005 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 779) hydrogen bonds : angle 4.18022 ( 2307) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.76969 ( 16) covalent geometry : bond 0.00264 (13975) covalent geometry : angle 0.65910 (19077) Misc. bond : bond 0.00637 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4139.67 seconds wall clock time: 72 minutes 36.11 seconds (4356.11 seconds total)