Starting phenix.real_space_refine on Sat Aug 23 17:49:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr9_49726/08_2025/9nr9_49726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr9_49726/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nr9_49726/08_2025/9nr9_49726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr9_49726/08_2025/9nr9_49726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nr9_49726/08_2025/9nr9_49726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr9_49726/08_2025/9nr9_49726.map" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'PHE:plan': 3} 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: {'ARG:plan': 2, 'PHE:plan': 3} 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: {'ARG:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 11, 'TYR:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 2} 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: {'GLU:plan': 10, 'PHE:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 10, 'ASP:plan': 4} 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: {'ARG:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 3, 'GLU:plan': 10, 'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 2} 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: {'ASN:plan1': 1, 'GLU:plan': 8, 'ASP:plan': 3, 'ARG:plan': 7, 'PHE:plan': 1} 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: 3.99, per 1000 atoms: 0.29 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: 1.15 Conformation dependent library (CDL) restraints added in 625.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 2.33 Time building geometry restraints manager: 1.53 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 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: 0.770 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.550 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B 487 TYR 0.014 0.001 TYR A 436 PHE 0.059 0.002 PHE F 141 TRP 0.016 0.001 TRP C 602 HIS 0.007 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00350 (13975) covalent geometry : angle 0.85446 (19077) SS BOND : bond 0.00090 ( 8) SS BOND : angle 1.65674 ( 16) hydrogen bonds : bond 0.13348 ( 779) hydrogen bonds : angle 6.04889 ( 2307) 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 : 0.512 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: 0.6844 (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: 0.6607 (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: 0.7874 (m-30) REVERT: C 761 LYS cc_start: 0.7832 (pptt) cc_final: 0.7126 (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: 0.8819 (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: 0.1063 time to fit residues: 53.7034 Evaluate side-chains 261 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.126708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102406 restraints weight = 48691.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103029 restraints weight = 37627.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103952 restraints weight = 28616.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103998 restraints weight = 23665.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.104018 restraints weight = 23846.423| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13985 Z= 0.112 Angle : 0.570 8.106 19093 Z= 0.287 Chirality : 0.039 0.190 2243 Planarity : 0.004 0.070 2354 Dihedral : 4.567 70.055 2068 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.15 % Allowed : 4.47 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 1833 helix: 1.20 (0.17), residues: 1002 sheet: -0.60 (0.58), residues: 88 loop : -2.23 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.010 0.001 TYR C 612 PHE 0.032 0.001 PHE H 182 TRP 0.007 0.001 TRP B 608 HIS 0.006 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00244 (13975) covalent geometry : angle 0.56939 (19077) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.82118 ( 16) hydrogen bonds : bond 0.03294 ( 779) hydrogen bonds : angle 4.40471 ( 2307) Misc. bond : bond 0.00540 ( 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 310 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 PHE cc_start: 0.7720 (m-80) cc_final: 0.7465 (m-80) REVERT: F 192 MET cc_start: 0.7969 (ppp) cc_final: 0.7691 (ppp) REVERT: A 434 TYR cc_start: 0.8214 (p90) cc_final: 0.7233 (p90) REVERT: A 524 CYS cc_start: 0.9014 (m) cc_final: 0.8496 (m) REVERT: A 605 THR cc_start: 0.9086 (p) cc_final: 0.8531 (t) REVERT: B 630 ARG cc_start: 0.7530 (mmt180) cc_final: 0.7226 (mmp80) REVERT: B 631 MET cc_start: 0.6079 (tpp) cc_final: 0.5852 (tpp) REVERT: B 772 LYS cc_start: 0.6730 (pttt) cc_final: 0.6384 (pttt) REVERT: B 791 LEU cc_start: 0.8781 (tp) cc_final: 0.8335 (tp) REVERT: C 400 PRO cc_start: 0.8949 (Cg_endo) cc_final: 0.8652 (Cg_exo) REVERT: C 434 TYR cc_start: 0.8017 (p90) cc_final: 0.6852 (p90) REVERT: C 479 LEU cc_start: 0.8700 (pt) cc_final: 0.8458 (mm) REVERT: C 756 ASP cc_start: 0.8340 (m-30) cc_final: 0.8059 (m-30) REVERT: D 529 MET cc_start: 0.7903 (pmm) cc_final: 0.7701 (pmm) REVERT: D 530 CYS cc_start: 0.9200 (m) cc_final: 0.8851 (m) REVERT: D 606 VAL cc_start: 0.9690 (m) cc_final: 0.9484 (p) REVERT: D 627 THR cc_start: 0.9224 (t) cc_final: 0.8919 (p) REVERT: D 716 GLN cc_start: 0.8220 (mm-40) cc_final: 0.7705 (tp40) REVERT: D 770 TYR cc_start: 0.7871 (m-80) cc_final: 0.7521 (m-10) REVERT: D 771 ASP cc_start: 0.7892 (m-30) cc_final: 0.7590 (m-30) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.1014 time to fit residues: 48.5481 Evaluate side-chains 240 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 0.3980 chunk 21 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 166 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 31 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN C 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.101722 restraints weight = 48336.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102052 restraints weight = 36347.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102799 restraints weight = 28084.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103545 restraints weight = 23515.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.103546 restraints weight = 21679.621| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13985 Z= 0.108 Angle : 0.558 7.793 19093 Z= 0.280 Chirality : 0.039 0.157 2243 Planarity : 0.004 0.064 2354 Dihedral : 4.406 60.167 2068 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.30 % Allowed : 3.87 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.20), residues: 1833 helix: 1.55 (0.17), residues: 1007 sheet: -0.33 (0.59), residues: 87 loop : -2.23 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 99 TYR 0.012 0.001 TYR B 407 PHE 0.017 0.001 PHE C 603 TRP 0.007 0.001 TRP B 608 HIS 0.003 0.000 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00231 (13975) covalent geometry : angle 0.55781 (19077) SS BOND : bond 0.00686 ( 8) SS BOND : angle 0.98063 ( 16) hydrogen bonds : bond 0.03085 ( 779) hydrogen bonds : angle 4.23245 ( 2307) Misc. bond : bond 0.00503 ( 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 309 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 305 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8319 (tpm170) cc_final: 0.7675 (tpm170) REVERT: F 130 THR cc_start: 0.8478 (t) cc_final: 0.8093 (p) REVERT: F 182 PHE cc_start: 0.7881 (m-80) cc_final: 0.7607 (m-80) REVERT: F 192 MET cc_start: 0.8149 (ppp) cc_final: 0.7896 (ppp) REVERT: A 434 TYR cc_start: 0.7887 (p90) cc_final: 0.6992 (p90) REVERT: A 524 CYS cc_start: 0.9033 (m) cc_final: 0.8511 (m) REVERT: A 605 THR cc_start: 0.9128 (p) cc_final: 0.8573 (t) REVERT: A 633 GLU cc_start: 0.9094 (pm20) cc_final: 0.8648 (pm20) REVERT: B 631 MET cc_start: 0.6302 (tpp) cc_final: 0.5970 (tpp) REVERT: B 772 LYS cc_start: 0.6555 (pttt) cc_final: 0.5724 (pttt) REVERT: B 791 LEU cc_start: 0.8822 (tp) cc_final: 0.8511 (tp) REVERT: C 399 ASP cc_start: 0.7765 (t0) cc_final: 0.7497 (t70) REVERT: C 400 PRO cc_start: 0.8800 (Cg_endo) cc_final: 0.8469 (Cg_exo) REVERT: C 434 TYR cc_start: 0.7970 (p90) cc_final: 0.6813 (p90) REVERT: C 479 LEU cc_start: 0.8682 (pt) cc_final: 0.8343 (mm) REVERT: C 756 ASP cc_start: 0.8374 (m-30) cc_final: 0.8128 (m-30) REVERT: C 759 LYS cc_start: 0.9167 (tttp) cc_final: 0.8816 (tptm) REVERT: D 529 MET cc_start: 0.7774 (pmm) cc_final: 0.7515 (pmm) REVERT: D 606 VAL cc_start: 0.9720 (m) cc_final: 0.9458 (p) REVERT: D 622 LEU cc_start: 0.9523 (tp) cc_final: 0.9293 (tp) REVERT: D 716 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7605 (tp40) REVERT: D 770 TYR cc_start: 0.7938 (m-80) cc_final: 0.7630 (m-10) REVERT: D 771 ASP cc_start: 0.7953 (m-30) cc_final: 0.7665 (m-30) outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.1036 time to fit residues: 49.0573 Evaluate side-chains 238 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 170 optimal weight: 0.0050 chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.121171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097251 restraints weight = 49005.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097294 restraints weight = 48289.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097991 restraints weight = 37885.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098211 restraints weight = 30634.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098473 restraints weight = 28644.667| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13985 Z= 0.144 Angle : 0.597 9.117 19093 Z= 0.304 Chirality : 0.040 0.158 2243 Planarity : 0.004 0.058 2354 Dihedral : 4.610 57.511 2068 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.23 % Allowed : 3.64 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1833 helix: 1.76 (0.17), residues: 1000 sheet: -0.39 (0.57), residues: 88 loop : -2.24 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 449 TYR 0.015 0.001 TYR B 770 PHE 0.022 0.002 PHE F 141 TRP 0.008 0.001 TRP D 768 HIS 0.003 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00319 (13975) covalent geometry : angle 0.59722 (19077) SS BOND : bond 0.00244 ( 8) SS BOND : angle 0.67481 ( 16) hydrogen bonds : bond 0.03319 ( 779) hydrogen bonds : angle 4.13919 ( 2307) Misc. bond : bond 0.00572 ( 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 297 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.7883 (tmm) cc_final: 0.7652 (tpt) REVERT: F 99 ARG cc_start: 0.8264 (tpm170) cc_final: 0.7660 (tpm170) REVERT: F 182 PHE cc_start: 0.7859 (m-80) cc_final: 0.7538 (m-80) REVERT: F 192 MET cc_start: 0.8102 (ppp) cc_final: 0.7760 (ppp) REVERT: F 199 HIS cc_start: 0.6437 (t70) cc_final: 0.6235 (t70) REVERT: H 174 TYR cc_start: 0.7153 (m-80) cc_final: 0.6189 (p90) REVERT: A 523 MET cc_start: 0.8371 (tmm) cc_final: 0.8151 (tmm) REVERT: A 524 CYS cc_start: 0.8967 (m) cc_final: 0.8435 (m) REVERT: A 605 THR cc_start: 0.9039 (p) cc_final: 0.8426 (t) REVERT: A 625 MET cc_start: 0.7924 (pmm) cc_final: 0.7658 (pmm) REVERT: A 633 GLU cc_start: 0.9052 (pm20) cc_final: 0.8457 (pm20) REVERT: B 631 MET cc_start: 0.6494 (tpp) cc_final: 0.5976 (tpp) REVERT: B 710 MET cc_start: 0.8689 (tpt) cc_final: 0.7711 (tpp) REVERT: B 772 LYS cc_start: 0.6605 (pttt) cc_final: 0.5866 (pttt) REVERT: B 791 LEU cc_start: 0.8969 (tp) cc_final: 0.8507 (tp) REVERT: C 399 ASP cc_start: 0.7789 (t0) cc_final: 0.7467 (t70) REVERT: C 756 ASP cc_start: 0.8283 (m-30) cc_final: 0.8037 (m-30) REVERT: D 529 MET cc_start: 0.7737 (pmm) cc_final: 0.7423 (pmm) REVERT: D 606 VAL cc_start: 0.9744 (m) cc_final: 0.9495 (p) REVERT: D 672 MET cc_start: 0.8527 (tmm) cc_final: 0.8266 (tpt) REVERT: D 716 GLN cc_start: 0.8464 (mm-40) cc_final: 0.7989 (tp-100) REVERT: D 770 TYR cc_start: 0.8347 (m-80) cc_final: 0.8086 (m-10) REVERT: D 771 ASP cc_start: 0.8194 (m-30) cc_final: 0.7974 (m-30) outliers start: 3 outliers final: 1 residues processed: 296 average time/residue: 0.1016 time to fit residues: 46.7752 Evaluate side-chains 235 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 91 optimal weight: 0.2980 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.122286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.099700 restraints weight = 49083.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101051 restraints weight = 41856.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101212 restraints weight = 34848.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.101262 restraints weight = 26777.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101481 restraints weight = 25572.512| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13985 Z= 0.116 Angle : 0.579 8.058 19093 Z= 0.290 Chirality : 0.039 0.152 2243 Planarity : 0.004 0.073 2354 Dihedral : 4.525 57.041 2068 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.15 % Allowed : 2.65 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1833 helix: 1.90 (0.17), residues: 1002 sheet: -0.60 (0.56), residues: 94 loop : -2.24 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.016 0.001 TYR B 407 PHE 0.025 0.001 PHE H 141 TRP 0.026 0.001 TRP B 768 HIS 0.003 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00263 (13975) covalent geometry : angle 0.57826 (19077) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.06038 ( 16) hydrogen bonds : bond 0.03100 ( 779) hydrogen bonds : angle 4.07983 ( 2307) Misc. bond : bond 0.00568 ( 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 296 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8154 (tpm170) cc_final: 0.7921 (tpm170) REVERT: F 130 THR cc_start: 0.8061 (t) cc_final: 0.7669 (p) REVERT: F 182 PHE cc_start: 0.7950 (m-80) cc_final: 0.7619 (m-80) REVERT: F 192 MET cc_start: 0.8002 (ppp) cc_final: 0.7683 (ppp) REVERT: F 199 HIS cc_start: 0.6124 (t70) cc_final: 0.5869 (t70) REVERT: A 434 TYR cc_start: 0.8055 (p90) cc_final: 0.7579 (p90) REVERT: A 524 CYS cc_start: 0.8553 (m) cc_final: 0.8118 (m) REVERT: A 605 THR cc_start: 0.8968 (p) cc_final: 0.8347 (t) REVERT: A 633 GLU cc_start: 0.9003 (pm20) cc_final: 0.8442 (pm20) REVERT: B 500 LEU cc_start: 0.9031 (mt) cc_final: 0.8669 (mp) REVERT: B 622 LEU cc_start: 0.9567 (tp) cc_final: 0.9125 (tp) REVERT: B 631 MET cc_start: 0.6460 (tpp) cc_final: 0.5874 (tpp) REVERT: B 710 MET cc_start: 0.8641 (tpt) cc_final: 0.7647 (tpp) REVERT: B 772 LYS cc_start: 0.6666 (pttt) cc_final: 0.5731 (pttt) REVERT: B 791 LEU cc_start: 0.8984 (tp) cc_final: 0.8541 (tp) REVERT: C 399 ASP cc_start: 0.7756 (t0) cc_final: 0.7452 (t0) REVERT: C 434 TYR cc_start: 0.7851 (p90) cc_final: 0.6766 (p90) REVERT: C 489 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8752 (mmtm) REVERT: C 606 LEU cc_start: 0.8695 (tp) cc_final: 0.8394 (tp) REVERT: C 756 ASP cc_start: 0.8332 (m-30) cc_final: 0.8120 (m-30) REVERT: C 757 LYS cc_start: 0.8884 (mttt) cc_final: 0.8660 (mttm) REVERT: D 606 VAL cc_start: 0.9703 (m) cc_final: 0.9440 (p) REVERT: D 716 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8139 (tp40) REVERT: D 770 TYR cc_start: 0.8293 (m-80) cc_final: 0.8075 (m-10) REVERT: D 771 ASP cc_start: 0.8149 (m-30) cc_final: 0.7938 (m-30) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.1013 time to fit residues: 46.5103 Evaluate side-chains 241 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 134 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 148 optimal weight: 0.0060 overall best weight: 0.6776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A 705 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.121696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.097834 restraints weight = 48664.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097807 restraints weight = 44215.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098583 restraints weight = 35160.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098750 restraints weight = 29287.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098858 restraints weight = 27974.871| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13985 Z= 0.115 Angle : 0.593 8.660 19093 Z= 0.294 Chirality : 0.039 0.158 2243 Planarity : 0.004 0.055 2354 Dihedral : 4.524 57.235 2068 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 0.15 % Allowed : 3.03 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1833 helix: 1.97 (0.17), residues: 1004 sheet: -0.64 (0.53), residues: 104 loop : -2.20 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.019 0.001 TYR B 407 PHE 0.045 0.001 PHE H 182 TRP 0.013 0.001 TRP B 768 HIS 0.003 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00258 (13975) covalent geometry : angle 0.59234 (19077) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.80249 ( 16) hydrogen bonds : bond 0.03072 ( 779) hydrogen bonds : angle 4.10661 ( 2307) Misc. bond : bond 0.00577 ( 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 291 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8279 (tpm170) cc_final: 0.7894 (tpm170) REVERT: F 130 THR cc_start: 0.8175 (t) cc_final: 0.7874 (p) REVERT: F 182 PHE cc_start: 0.8018 (m-80) cc_final: 0.7663 (m-80) REVERT: F 187 PHE cc_start: 0.8547 (t80) cc_final: 0.7663 (t80) REVERT: F 192 MET cc_start: 0.8271 (ppp) cc_final: 0.7952 (ppp) REVERT: F 199 HIS cc_start: 0.6104 (t70) cc_final: 0.5884 (t70) REVERT: H 192 MET cc_start: 0.7499 (ppp) cc_final: 0.6989 (ppp) REVERT: A 420 TYR cc_start: 0.8148 (t80) cc_final: 0.7764 (t80) REVERT: A 434 TYR cc_start: 0.8171 (p90) cc_final: 0.7673 (p90) REVERT: A 524 CYS cc_start: 0.8447 (m) cc_final: 0.8001 (m) REVERT: A 605 THR cc_start: 0.8928 (p) cc_final: 0.8355 (t) REVERT: A 633 GLU cc_start: 0.9004 (pm20) cc_final: 0.8448 (pm20) REVERT: A 634 ASP cc_start: 0.8654 (t0) cc_final: 0.8452 (t0) REVERT: B 622 LEU cc_start: 0.9559 (tp) cc_final: 0.9179 (tp) REVERT: B 631 MET cc_start: 0.6667 (tpp) cc_final: 0.6108 (tpp) REVERT: B 710 MET cc_start: 0.8669 (tpt) cc_final: 0.8127 (tpp) REVERT: B 791 LEU cc_start: 0.8926 (tp) cc_final: 0.8643 (tp) REVERT: C 399 ASP cc_start: 0.7718 (t0) cc_final: 0.7450 (t0) REVERT: C 515 ASP cc_start: 0.9209 (t70) cc_final: 0.8939 (t0) REVERT: C 606 LEU cc_start: 0.8673 (tp) cc_final: 0.8186 (tp) REVERT: C 703 THR cc_start: 0.9077 (m) cc_final: 0.8852 (m) REVERT: C 757 LYS cc_start: 0.8716 (mttt) cc_final: 0.8475 (mttm) REVERT: D 606 VAL cc_start: 0.9707 (m) cc_final: 0.9454 (p) REVERT: D 622 LEU cc_start: 0.9360 (tp) cc_final: 0.9077 (tp) REVERT: D 716 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8070 (tp-100) outliers start: 2 outliers final: 0 residues processed: 291 average time/residue: 0.0974 time to fit residues: 43.9194 Evaluate side-chains 239 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 84 optimal weight: 0.0170 chunk 140 optimal weight: 0.0970 chunk 182 optimal weight: 7.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.121999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098699 restraints weight = 47765.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098794 restraints weight = 48962.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099778 restraints weight = 36074.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100084 restraints weight = 27711.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100269 restraints weight = 26107.999| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13985 Z= 0.113 Angle : 0.602 8.700 19093 Z= 0.298 Chirality : 0.040 0.210 2243 Planarity : 0.004 0.053 2354 Dihedral : 4.505 56.934 2068 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.15 % Allowed : 1.44 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1833 helix: 1.98 (0.17), residues: 1005 sheet: -0.63 (0.54), residues: 104 loop : -2.22 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.015 0.001 TYR B 407 PHE 0.043 0.001 PHE H 182 TRP 0.011 0.001 TRP B 768 HIS 0.003 0.001 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00253 (13975) covalent geometry : angle 0.60199 (19077) SS BOND : bond 0.00242 ( 8) SS BOND : angle 1.04846 ( 16) hydrogen bonds : bond 0.03020 ( 779) hydrogen bonds : angle 4.12170 ( 2307) Misc. bond : bond 0.00574 ( 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 288 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 286 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8242 (tpm170) cc_final: 0.7889 (tpm170) REVERT: F 130 THR cc_start: 0.8045 (t) cc_final: 0.7723 (p) REVERT: F 182 PHE cc_start: 0.8003 (m-80) cc_final: 0.7649 (m-80) REVERT: F 192 MET cc_start: 0.8015 (ppp) cc_final: 0.7689 (ppp) REVERT: H 192 MET cc_start: 0.6854 (ppp) cc_final: 0.6603 (ppp) REVERT: A 420 TYR cc_start: 0.8026 (t80) cc_final: 0.7751 (t80) REVERT: A 524 CYS cc_start: 0.8563 (m) cc_final: 0.8146 (m) REVERT: A 605 THR cc_start: 0.8818 (p) cc_final: 0.8200 (t) REVERT: A 633 GLU cc_start: 0.8999 (pm20) cc_final: 0.8434 (pm20) REVERT: A 634 ASP cc_start: 0.8615 (t0) cc_final: 0.8404 (t0) REVERT: B 622 LEU cc_start: 0.9505 (tp) cc_final: 0.9105 (tp) REVERT: B 631 MET cc_start: 0.6835 (tpp) cc_final: 0.6285 (tpp) REVERT: B 710 MET cc_start: 0.9036 (tpt) cc_final: 0.7824 (tpp) REVERT: B 772 LYS cc_start: 0.7219 (pttt) cc_final: 0.6422 (pttt) REVERT: B 791 LEU cc_start: 0.8967 (tp) cc_final: 0.8661 (tp) REVERT: C 399 ASP cc_start: 0.7646 (t0) cc_final: 0.7399 (t70) REVERT: C 434 TYR cc_start: 0.8026 (p90) cc_final: 0.6852 (p90) REVERT: C 515 ASP cc_start: 0.9225 (t70) cc_final: 0.8926 (t0) REVERT: C 606 LEU cc_start: 0.8666 (tp) cc_final: 0.8025 (tp) REVERT: C 756 ASP cc_start: 0.8303 (m-30) cc_final: 0.8066 (m-30) REVERT: C 757 LYS cc_start: 0.8868 (mttt) cc_final: 0.8637 (mttm) REVERT: D 505 MET cc_start: 0.8950 (ptm) cc_final: 0.8630 (ptm) REVERT: D 606 VAL cc_start: 0.9695 (m) cc_final: 0.9441 (p) REVERT: D 622 LEU cc_start: 0.9412 (tp) cc_final: 0.9132 (tp) REVERT: D 716 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8077 (tp-100) REVERT: D 770 TYR cc_start: 0.8431 (m-80) cc_final: 0.7631 (m-10) REVERT: D 771 ASP cc_start: 0.8175 (m-30) cc_final: 0.7956 (m-30) outliers start: 2 outliers final: 0 residues processed: 288 average time/residue: 0.0890 time to fit residues: 40.4575 Evaluate side-chains 236 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 32 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 133 optimal weight: 0.0870 chunk 117 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.121955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098824 restraints weight = 48365.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.098451 restraints weight = 48124.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099198 restraints weight = 38071.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.099412 restraints weight = 30251.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099511 restraints weight = 29146.977| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13985 Z= 0.114 Angle : 0.604 8.571 19093 Z= 0.299 Chirality : 0.040 0.204 2243 Planarity : 0.004 0.053 2354 Dihedral : 4.515 56.582 2068 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.20), residues: 1833 helix: 1.95 (0.16), residues: 1008 sheet: -0.70 (0.54), residues: 104 loop : -2.20 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 65 TYR 0.015 0.001 TYR B 407 PHE 0.042 0.001 PHE H 182 TRP 0.009 0.001 TRP B 768 HIS 0.002 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00256 (13975) covalent geometry : angle 0.60412 (19077) SS BOND : bond 0.00188 ( 8) SS BOND : angle 0.90459 ( 16) hydrogen bonds : bond 0.03027 ( 779) hydrogen bonds : angle 4.08297 ( 2307) Misc. bond : bond 0.00582 ( 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 283 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8230 (tpm170) cc_final: 0.7874 (tpm170) REVERT: F 182 PHE cc_start: 0.8249 (m-80) cc_final: 0.7869 (m-80) REVERT: F 187 PHE cc_start: 0.8474 (t80) cc_final: 0.7619 (t80) REVERT: F 192 MET cc_start: 0.8131 (ppp) cc_final: 0.7871 (ppp) REVERT: H 189 ILE cc_start: 0.8428 (tt) cc_final: 0.8199 (tt) REVERT: A 420 TYR cc_start: 0.8189 (t80) cc_final: 0.7674 (t80) REVERT: A 434 TYR cc_start: 0.7969 (p90) cc_final: 0.7767 (p90) REVERT: A 523 MET cc_start: 0.8500 (tmm) cc_final: 0.8185 (tmm) REVERT: A 524 CYS cc_start: 0.8691 (m) cc_final: 0.8332 (m) REVERT: A 527 PHE cc_start: 0.8535 (m-80) cc_final: 0.8310 (m-10) REVERT: A 605 THR cc_start: 0.8918 (p) cc_final: 0.8360 (t) REVERT: A 625 MET cc_start: 0.8343 (pmm) cc_final: 0.8008 (pmm) REVERT: A 633 GLU cc_start: 0.8738 (pm20) cc_final: 0.8248 (pm20) REVERT: A 634 ASP cc_start: 0.8582 (t0) cc_final: 0.8352 (t0) REVERT: B 622 LEU cc_start: 0.9532 (tp) cc_final: 0.9159 (tp) REVERT: B 631 MET cc_start: 0.6946 (tpp) cc_final: 0.6382 (tpp) REVERT: B 710 MET cc_start: 0.8989 (tpt) cc_final: 0.7760 (tpp) REVERT: B 772 LYS cc_start: 0.7205 (pttt) cc_final: 0.6438 (pttt) REVERT: B 791 LEU cc_start: 0.8919 (tp) cc_final: 0.8646 (tp) REVERT: C 399 ASP cc_start: 0.7716 (t0) cc_final: 0.7446 (t70) REVERT: C 606 LEU cc_start: 0.8442 (tp) cc_final: 0.7877 (tp) REVERT: C 703 THR cc_start: 0.9081 (m) cc_final: 0.8859 (m) REVERT: C 757 LYS cc_start: 0.8687 (mttt) cc_final: 0.8385 (mttm) REVERT: C 759 LYS cc_start: 0.9098 (tttp) cc_final: 0.8598 (tptm) REVERT: C 761 LYS cc_start: 0.8153 (pptt) cc_final: 0.7487 (pttm) REVERT: D 505 MET cc_start: 0.8943 (ptm) cc_final: 0.8658 (ptm) REVERT: D 606 VAL cc_start: 0.9686 (m) cc_final: 0.9438 (p) REVERT: D 622 LEU cc_start: 0.9560 (tp) cc_final: 0.9219 (tp) REVERT: D 716 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8273 (tp-100) REVERT: D 770 TYR cc_start: 0.8507 (m-80) cc_final: 0.7754 (m-10) outliers start: 2 outliers final: 1 residues processed: 283 average time/residue: 0.0991 time to fit residues: 43.9636 Evaluate side-chains 240 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 115 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 0.0570 chunk 164 optimal weight: 0.0020 chunk 91 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.099920 restraints weight = 48635.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.099821 restraints weight = 49876.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.100982 restraints weight = 39470.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101303 restraints weight = 29562.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101558 restraints weight = 27948.736| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 13985 Z= 0.110 Angle : 0.615 8.558 19093 Z= 0.302 Chirality : 0.040 0.201 2243 Planarity : 0.004 0.070 2354 Dihedral : 4.514 56.011 2068 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 0.83 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.20), residues: 1833 helix: 2.02 (0.16), residues: 1004 sheet: -0.86 (0.55), residues: 98 loop : -2.16 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 65 TYR 0.023 0.001 TYR H 174 PHE 0.040 0.001 PHE H 182 TRP 0.008 0.001 TRP C 522 HIS 0.002 0.000 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00248 (13975) covalent geometry : angle 0.61503 (19077) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.81190 ( 16) hydrogen bonds : bond 0.02923 ( 779) hydrogen bonds : angle 4.08487 ( 2307) Misc. bond : bond 0.00541 ( 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 292 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8249 (tpm170) cc_final: 0.7898 (tpm170) REVERT: F 182 PHE cc_start: 0.8228 (m-80) cc_final: 0.7856 (m-80) REVERT: F 187 PHE cc_start: 0.8524 (t80) cc_final: 0.7503 (t80) REVERT: F 192 MET cc_start: 0.8216 (ppp) cc_final: 0.7946 (ppp) REVERT: F 200 MET cc_start: 0.3690 (mtt) cc_final: 0.3404 (mtm) REVERT: H 192 MET cc_start: 0.8220 (tmm) cc_final: 0.7831 (ppp) REVERT: A 434 TYR cc_start: 0.7960 (p90) cc_final: 0.7723 (p90) REVERT: A 523 MET cc_start: 0.8540 (tmm) cc_final: 0.8229 (tmm) REVERT: A 524 CYS cc_start: 0.8778 (m) cc_final: 0.8336 (m) REVERT: A 527 PHE cc_start: 0.8554 (m-80) cc_final: 0.8330 (m-10) REVERT: A 605 THR cc_start: 0.8774 (p) cc_final: 0.8188 (t) REVERT: A 625 MET cc_start: 0.7988 (pmm) cc_final: 0.7031 (pmm) REVERT: A 633 GLU cc_start: 0.8536 (pm20) cc_final: 0.8038 (pm20) REVERT: A 634 ASP cc_start: 0.8517 (t0) cc_final: 0.8287 (t0) REVERT: B 622 LEU cc_start: 0.9462 (tp) cc_final: 0.9039 (tp) REVERT: B 631 MET cc_start: 0.6947 (tpp) cc_final: 0.6377 (tpp) REVERT: B 710 MET cc_start: 0.9000 (tpt) cc_final: 0.7996 (tpp) REVERT: B 767 LYS cc_start: 0.7725 (pptt) cc_final: 0.7454 (pptt) REVERT: B 772 LYS cc_start: 0.7276 (pttt) cc_final: 0.6636 (pttt) REVERT: B 791 LEU cc_start: 0.8920 (tp) cc_final: 0.8635 (tp) REVERT: C 399 ASP cc_start: 0.7588 (t0) cc_final: 0.7369 (t70) REVERT: C 434 TYR cc_start: 0.8028 (p90) cc_final: 0.6862 (p90) REVERT: C 515 ASP cc_start: 0.8887 (t70) cc_final: 0.8671 (t70) REVERT: C 606 LEU cc_start: 0.8770 (tp) cc_final: 0.8253 (tp) REVERT: C 759 LYS cc_start: 0.9132 (tttp) cc_final: 0.8668 (tptm) REVERT: C 799 LEU cc_start: 0.9257 (mm) cc_final: 0.9057 (mm) REVERT: D 505 MET cc_start: 0.8982 (ptm) cc_final: 0.8776 (ptm) REVERT: D 606 VAL cc_start: 0.9651 (m) cc_final: 0.9399 (p) REVERT: D 622 LEU cc_start: 0.9344 (tp) cc_final: 0.9022 (tp) REVERT: D 716 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8443 (tp-100) REVERT: D 770 TYR cc_start: 0.8497 (m-80) cc_final: 0.7748 (m-10) REVERT: D 771 ASP cc_start: 0.8146 (m-30) cc_final: 0.7937 (m-30) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.1006 time to fit residues: 45.6182 Evaluate side-chains 242 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 95 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.0000 chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 180 optimal weight: 0.0970 chunk 129 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.122234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099354 restraints weight = 48817.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098702 restraints weight = 45817.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099481 restraints weight = 39588.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099904 restraints weight = 30275.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.100002 restraints weight = 28387.605| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13985 Z= 0.119 Angle : 0.645 10.606 19093 Z= 0.317 Chirality : 0.040 0.190 2243 Planarity : 0.004 0.062 2354 Dihedral : 4.483 56.193 2068 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.20), residues: 1833 helix: 2.04 (0.17), residues: 1008 sheet: -0.68 (0.53), residues: 103 loop : -2.16 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 449 TYR 0.019 0.001 TYR H 174 PHE 0.029 0.001 PHE H 187 TRP 0.009 0.001 TRP D 768 HIS 0.003 0.000 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00271 (13975) covalent geometry : angle 0.64483 (19077) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.79168 ( 16) hydrogen bonds : bond 0.02967 ( 779) hydrogen bonds : angle 4.14149 ( 2307) Misc. bond : bond 0.00543 ( 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 285 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 99 ARG cc_start: 0.8289 (tpm170) cc_final: 0.7911 (tpm170) REVERT: F 182 PHE cc_start: 0.8293 (m-80) cc_final: 0.7902 (m-80) REVERT: F 187 PHE cc_start: 0.8560 (t80) cc_final: 0.7504 (t80) REVERT: F 192 MET cc_start: 0.8216 (ppp) cc_final: 0.7955 (ppp) REVERT: F 200 MET cc_start: 0.3721 (mtt) cc_final: 0.3423 (mtm) REVERT: A 434 TYR cc_start: 0.8023 (p90) cc_final: 0.7780 (p90) REVERT: A 523 MET cc_start: 0.8513 (tmm) cc_final: 0.8182 (tmm) REVERT: A 524 CYS cc_start: 0.8765 (m) cc_final: 0.8313 (m) REVERT: A 527 PHE cc_start: 0.8604 (m-80) cc_final: 0.8355 (m-10) REVERT: A 605 THR cc_start: 0.8837 (p) cc_final: 0.8292 (t) REVERT: A 625 MET cc_start: 0.8433 (pmm) cc_final: 0.7286 (pmm) REVERT: A 633 GLU cc_start: 0.8810 (pm20) cc_final: 0.8200 (pm20) REVERT: A 634 ASP cc_start: 0.8500 (t0) cc_final: 0.8289 (t0) REVERT: A 676 SER cc_start: 0.7762 (m) cc_final: 0.7536 (t) REVERT: A 686 MET cc_start: 0.7555 (mpp) cc_final: 0.7350 (mtm) REVERT: B 622 LEU cc_start: 0.9297 (tp) cc_final: 0.8998 (tp) REVERT: B 631 MET cc_start: 0.7072 (tpp) cc_final: 0.6527 (tpp) REVERT: B 710 MET cc_start: 0.9019 (tpt) cc_final: 0.7998 (tpp) REVERT: B 772 LYS cc_start: 0.7288 (pttt) cc_final: 0.6665 (pttt) REVERT: B 791 LEU cc_start: 0.8911 (tp) cc_final: 0.8653 (tp) REVERT: C 399 ASP cc_start: 0.7660 (t0) cc_final: 0.7397 (t70) REVERT: C 606 LEU cc_start: 0.8663 (tp) cc_final: 0.8143 (tp) REVERT: C 703 THR cc_start: 0.9075 (m) cc_final: 0.8838 (m) REVERT: C 759 LYS cc_start: 0.9071 (tttp) cc_final: 0.8613 (tptm) REVERT: D 505 MET cc_start: 0.8865 (ptm) cc_final: 0.8610 (ptm) REVERT: D 606 VAL cc_start: 0.9656 (m) cc_final: 0.9398 (p) REVERT: D 622 LEU cc_start: 0.9589 (tp) cc_final: 0.9246 (tp) REVERT: D 716 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8402 (tp-100) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.0979 time to fit residues: 43.7604 Evaluate side-chains 239 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 159 optimal weight: 0.0980 chunk 168 optimal weight: 4.9990 chunk 131 optimal weight: 0.0170 chunk 180 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100063 restraints weight = 48189.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099684 restraints weight = 45666.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.100422 restraints weight = 37363.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.100677 restraints weight = 30420.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.100820 restraints weight = 29205.396| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 13985 Z= 0.109 Angle : 0.633 10.536 19093 Z= 0.310 Chirality : 0.040 0.191 2243 Planarity : 0.004 0.056 2354 Dihedral : 4.471 57.708 2068 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.08 % Allowed : 0.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1833 helix: 2.07 (0.16), residues: 1005 sheet: -0.60 (0.57), residues: 93 loop : -2.10 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 65 TYR 0.018 0.001 TYR H 174 PHE 0.026 0.001 PHE H 141 TRP 0.030 0.001 TRP D 528 HIS 0.003 0.000 HIS H 199 Details of bonding type rmsd covalent geometry : bond 0.00246 (13975) covalent geometry : angle 0.63317 (19077) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.80583 ( 16) hydrogen bonds : bond 0.02865 ( 779) hydrogen bonds : angle 4.12056 ( 2307) Misc. bond : bond 0.00531 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.22 seconds wall clock time: 39 minutes 48.61 seconds (2388.61 seconds total)