Starting phenix.real_space_refine on Tue Nov 18 16:13:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhb_13969/11_2025/7qhb_13969.map" } resolution = 3.5 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 94 5.16 5 Cl 4 4.86 5 C 9886 2.51 5 N 2374 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15052 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 13, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'TYR:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "I" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {'79N': 1, 'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU A1202 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {'79N': 2, 'CYZ': 1, 'PAM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, D Time building chain proxies: 4.59, per 1000 atoms: 0.30 Number of scatterers: 15052 At special positions: 0 Unit cell: (126.14, 107.06, 134.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 94 16.00 O 2694 8.00 N 2374 7.00 C 9886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " 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=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 635.8 milliseconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 56.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.639A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 789 through 815 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.718A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.640A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 789 through 815 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.717A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 Processing helix chain 'I' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 151 Processing helix chain 'J' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 439 through 444 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 439 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 45 through 49 removed outlier: 3.867A pdb=" N HIS I 83 " --> pdb=" O CYS I 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.868A pdb=" N HIS J 83 " --> pdb=" O CYS J 90 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2550 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: 2.34 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2348 1.31 - 1.44: 4367 1.44 - 1.57: 8485 1.57 - 1.71: 8 1.71 - 1.84: 146 Bond restraints: 15354 Sorted by residual: bond pdb=" CB THR C 605 " pdb=" CG2 THR C 605 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CG LEU B 789 " pdb=" CD1 LEU B 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CG LEU D 789 " pdb=" CD1 LEU D 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CB THR A 605 " pdb=" CG2 THR A 605 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 bond pdb=" CB THR B 609 " pdb=" CG2 THR B 609 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 20101 2.71 - 5.43: 567 5.43 - 8.14: 92 8.14 - 10.85: 10 10.85 - 13.57: 2 Bond angle restraints: 20772 Sorted by residual: angle pdb=" C10 79N B 904 " pdb=" C9 79N B 904 " pdb=" C8 79N B 904 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C10 79N A1206 " pdb=" C9 79N A1206 " pdb=" C8 79N A1206 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N SER D 741 " pdb=" CA SER D 741 " pdb=" C SER D 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N SER B 741 " pdb=" CA SER B 741 " pdb=" C SER B 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CG ARG J 122 " pdb=" CD ARG J 122 " pdb=" NE ARG J 122 " ideal model delta sigma weight residual 112.00 119.81 -7.81 2.20e+00 2.07e-01 1.26e+01 ... (remaining 20767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 8457 24.73 - 49.45: 465 49.45 - 74.18: 74 74.18 - 98.90: 18 98.90 - 123.63: 20 Dihedral angle restraints: 9034 sinusoidal: 3420 harmonic: 5614 Sorted by residual: dihedral pdb=" C THR B 744 " pdb=" N THR B 744 " pdb=" CA THR B 744 " pdb=" CB THR B 744 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.07e+01 dihedral pdb=" C THR D 744 " pdb=" N THR D 744 " pdb=" CA THR D 744 " pdb=" CB THR D 744 " ideal model delta harmonic sigma weight residual -122.00 -133.30 11.30 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" N2 CYZ A1203 " pdb=" C8 CYZ A1203 " pdb=" N1 CYZ A1203 " pdb=" S1 CYZ A1203 " ideal model delta sinusoidal sigma weight residual 55.73 -67.90 123.63 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1989 0.084 - 0.168: 332 0.168 - 0.252: 65 0.252 - 0.336: 4 0.336 - 0.420: 4 Chirality restraints: 2394 Sorted by residual: chirality pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C6 CYZ B 902 " pdb=" C8 CYZ B 902 " both_signs ideal model delta sigma weight residual False 2.79 2.37 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C6 CYZ D 902 " pdb=" C8 CYZ D 902 " both_signs ideal model delta sigma weight residual False 2.79 2.38 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB THR C 605 " pdb=" CA THR C 605 " pdb=" OG1 THR C 605 " pdb=" CG2 THR C 605 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2391 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP J 111 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" CG ASP J 111 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP J 111 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 111 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 111 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" CG ASP I 111 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP I 111 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP I 111 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO D 404 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 176 2.60 - 3.18: 14752 3.18 - 3.75: 23237 3.75 - 4.33: 32386 4.33 - 4.90: 54353 Nonbonded interactions: 124904 Sorted by model distance: nonbonded pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS I 90 " pdb=" SG CYS I 100 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS J 90 " pdb=" SG CYS J 100 " model vdw 2.036 3.760 nonbonded pdb=" O1 79N D 903 " pdb=" O3 79N D 903 " model vdw 2.144 3.040 ... (remaining 124899 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 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'B' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) selection = (chain 'C' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'D' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.018 0.146 15358 Z= 0.701 Angle : 1.050 13.568 20780 Z= 0.535 Chirality : 0.068 0.420 2394 Planarity : 0.005 0.058 2544 Dihedral : 17.095 123.629 5438 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.55 % Allowed : 0.69 % Favored : 98.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: -2.00 (0.18), residues: 1926 helix: -0.28 (0.15), residues: 1056 sheet: -2.63 (0.35), residues: 172 loop : -2.55 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG J 122 TYR 0.039 0.003 TYR B 700 PHE 0.023 0.003 PHE D 541 TRP 0.010 0.002 TRP B 605 HIS 0.007 0.002 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.01755 (15354) covalent geometry : angle 1.04990 (20772) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.80312 ( 8) hydrogen bonds : bond 0.14113 ( 878) hydrogen bonds : angle 6.93624 ( 2550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 284 time to evaluate : 0.534 Fit side-chains REVERT: B 591 ILE cc_start: 0.7825 (tp) cc_final: 0.7591 (tp) REVERT: B 642 GLN cc_start: 0.7292 (pp30) cc_final: 0.6871 (pp30) REVERT: B 766 TRP cc_start: 0.6293 (m100) cc_final: 0.6048 (m100) REVERT: D 591 ILE cc_start: 0.7818 (tp) cc_final: 0.7575 (tp) REVERT: D 642 GLN cc_start: 0.7290 (pp30) cc_final: 0.6869 (pp30) REVERT: D 766 TRP cc_start: 0.6330 (m100) cc_final: 0.6035 (m100) outliers start: 8 outliers final: 2 residues processed: 286 average time/residue: 0.1147 time to fit residues: 49.9011 Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN I 105 HIS I 172 ASN ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 105 HIS ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.208378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.180303 restraints weight = 18263.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180409 restraints weight = 37890.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181164 restraints weight = 30774.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.183030 restraints weight = 20096.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183117 restraints weight = 17448.979| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15358 Z= 0.160 Angle : 0.610 9.697 20780 Z= 0.314 Chirality : 0.044 0.204 2394 Planarity : 0.005 0.044 2544 Dihedral : 13.469 101.678 2518 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.10 % Allowed : 9.81 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 0.23 (0.20), residues: 1926 helix: 1.65 (0.16), residues: 1070 sheet: -2.76 (0.35), residues: 166 loop : -1.50 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 48 TYR 0.017 0.002 TYR C 401 PHE 0.011 0.001 PHE C 542 TRP 0.010 0.001 TRP B 605 HIS 0.013 0.002 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00372 (15354) covalent geometry : angle 0.60987 (20772) SS BOND : bond 0.00712 ( 4) SS BOND : angle 0.45228 ( 8) hydrogen bonds : bond 0.03945 ( 878) hydrogen bonds : angle 4.47445 ( 2550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8322 (mm) cc_final: 0.7922 (pt) REVERT: A 812 TYR cc_start: 0.6403 (t80) cc_final: 0.6163 (t80) REVERT: A 813 LYS cc_start: 0.6093 (mtpp) cc_final: 0.5219 (tttt) REVERT: B 642 GLN cc_start: 0.7495 (pp30) cc_final: 0.6991 (pp30) REVERT: B 674 MET cc_start: 0.7369 (ptm) cc_final: 0.7095 (ptm) REVERT: B 766 TRP cc_start: 0.5879 (m100) cc_final: 0.5524 (m100) REVERT: C 496 ILE cc_start: 0.8331 (mm) cc_final: 0.7933 (pt) REVERT: C 711 ARG cc_start: 0.3309 (mmp-170) cc_final: 0.3040 (mmp80) REVERT: C 812 TYR cc_start: 0.6411 (t80) cc_final: 0.6162 (t80) REVERT: C 813 LYS cc_start: 0.6128 (mtpp) cc_final: 0.5256 (tttt) REVERT: D 642 GLN cc_start: 0.7500 (pp30) cc_final: 0.6995 (pp30) REVERT: D 674 MET cc_start: 0.7342 (ptm) cc_final: 0.7133 (ptm) REVERT: D 766 TRP cc_start: 0.5880 (m100) cc_final: 0.5530 (m100) REVERT: I 42 ASP cc_start: 0.7315 (p0) cc_final: 0.6294 (p0) REVERT: J 42 ASP cc_start: 0.7237 (p0) cc_final: 0.6206 (p0) REVERT: J 122 ARG cc_start: 0.7482 (mtp180) cc_final: 0.7242 (mmt180) outliers start: 16 outliers final: 6 residues processed: 289 average time/residue: 0.1239 time to fit residues: 53.6978 Evaluate side-chains 254 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 127 optimal weight: 0.0570 chunk 185 optimal weight: 4.9990 chunk 106 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 105 HIS I 197 ASN J 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.208004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.178672 restraints weight = 18397.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178791 restraints weight = 38604.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180180 restraints weight = 31366.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.181038 restraints weight = 20028.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181607 restraints weight = 17479.711| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15358 Z= 0.127 Angle : 0.529 8.770 20780 Z= 0.272 Chirality : 0.041 0.155 2394 Planarity : 0.004 0.040 2544 Dihedral : 12.207 92.388 2518 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 11.81 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 0.92 (0.20), residues: 1926 helix: 2.18 (0.16), residues: 1072 sheet: -2.40 (0.37), residues: 146 loop : -1.21 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 657 TYR 0.016 0.001 TYR C 401 PHE 0.010 0.001 PHE I 130 TRP 0.011 0.001 TRP B 460 HIS 0.010 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00293 (15354) covalent geometry : angle 0.52912 (20772) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.54136 ( 8) hydrogen bonds : bond 0.03506 ( 878) hydrogen bonds : angle 4.12116 ( 2550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.482 Fit side-chains REVERT: A 469 ASP cc_start: 0.5404 (m-30) cc_final: 0.4379 (m-30) REVERT: A 717 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6981 (ttp) REVERT: A 812 TYR cc_start: 0.6431 (t80) cc_final: 0.6230 (t80) REVERT: B 642 GLN cc_start: 0.7420 (pp30) cc_final: 0.7006 (pp30) REVERT: B 674 MET cc_start: 0.7463 (ptm) cc_final: 0.7257 (ptm) REVERT: B 708 MET cc_start: 0.7156 (mtt) cc_final: 0.6863 (mtt) REVERT: C 469 ASP cc_start: 0.5386 (m-30) cc_final: 0.4346 (m-30) REVERT: C 812 TYR cc_start: 0.6438 (t80) cc_final: 0.6227 (t80) REVERT: D 642 GLN cc_start: 0.7396 (pp30) cc_final: 0.6969 (pp30) REVERT: D 674 MET cc_start: 0.7419 (ptm) cc_final: 0.7206 (ptm) REVERT: D 708 MET cc_start: 0.7157 (mtt) cc_final: 0.6869 (mtt) REVERT: I 227 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7603 (mp) REVERT: J 103 ILE cc_start: 0.8249 (mt) cc_final: 0.8041 (mt) outliers start: 31 outliers final: 16 residues processed: 284 average time/residue: 0.1207 time to fit residues: 51.6296 Evaluate side-chains 277 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 139 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 135 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.204913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172176 restraints weight = 18201.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160401 restraints weight = 24524.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159707 restraints weight = 29486.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.159929 restraints weight = 24782.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160099 restraints weight = 20927.559| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15358 Z= 0.157 Angle : 0.552 6.659 20780 Z= 0.283 Chirality : 0.041 0.150 2394 Planarity : 0.004 0.042 2544 Dihedral : 11.562 79.599 2518 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.86 % Allowed : 12.98 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.00 (0.20), residues: 1926 helix: 2.16 (0.16), residues: 1072 sheet: -2.22 (0.37), residues: 152 loop : -1.04 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 48 TYR 0.018 0.001 TYR C 401 PHE 0.013 0.001 PHE D 515 TRP 0.010 0.001 TRP C 762 HIS 0.009 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00376 (15354) covalent geometry : angle 0.55166 (20772) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.32491 ( 8) hydrogen bonds : bond 0.03553 ( 878) hydrogen bonds : angle 4.11674 ( 2550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.560 Fit side-chains REVERT: A 469 ASP cc_start: 0.6175 (m-30) cc_final: 0.5088 (m-30) REVERT: A 717 MET cc_start: 0.7315 (ptt) cc_final: 0.7072 (ttp) REVERT: A 813 LYS cc_start: 0.5820 (mtpp) cc_final: 0.4821 (tttt) REVERT: B 483 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7979 (tt) REVERT: B 642 GLN cc_start: 0.7647 (pp30) cc_final: 0.7015 (pp30) REVERT: B 708 MET cc_start: 0.7222 (mtt) cc_final: 0.6926 (mtt) REVERT: C 469 ASP cc_start: 0.6173 (m-30) cc_final: 0.5062 (m-30) REVERT: C 813 LYS cc_start: 0.5807 (mtpp) cc_final: 0.4791 (tttt) REVERT: D 483 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7972 (tt) REVERT: D 642 GLN cc_start: 0.7662 (pp30) cc_final: 0.7036 (pp30) REVERT: D 708 MET cc_start: 0.7227 (mtt) cc_final: 0.6929 (mtt) REVERT: I 42 ASP cc_start: 0.6945 (p0) cc_final: 0.6693 (p0) REVERT: I 48 ARG cc_start: 0.7215 (ttm110) cc_final: 0.7011 (ttm-80) REVERT: I 103 ILE cc_start: 0.8264 (mt) cc_final: 0.7987 (mt) REVERT: I 227 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7565 (mp) REVERT: J 42 ASP cc_start: 0.6978 (p0) cc_final: 0.6743 (p0) REVERT: J 48 ARG cc_start: 0.7251 (ttm110) cc_final: 0.7002 (ttm-80) REVERT: J 103 ILE cc_start: 0.8449 (mt) cc_final: 0.8101 (mt) outliers start: 27 outliers final: 14 residues processed: 295 average time/residue: 0.1179 time to fit residues: 52.6543 Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain I residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN B 756 GLN C 571 ASN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN J 105 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.205500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173993 restraints weight = 18297.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173683 restraints weight = 37492.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174806 restraints weight = 34600.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.177264 restraints weight = 21193.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177428 restraints weight = 15991.745| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15358 Z= 0.133 Angle : 0.543 10.215 20780 Z= 0.272 Chirality : 0.041 0.206 2394 Planarity : 0.004 0.041 2544 Dihedral : 10.736 63.016 2518 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.21 % Allowed : 13.47 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.10 (0.20), residues: 1926 helix: 2.19 (0.16), residues: 1076 sheet: -2.06 (0.35), residues: 160 loop : -0.93 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 711 TYR 0.015 0.001 TYR A 401 PHE 0.013 0.001 PHE D 515 TRP 0.008 0.001 TRP C 762 HIS 0.009 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00312 (15354) covalent geometry : angle 0.54232 (20772) SS BOND : bond 0.00086 ( 4) SS BOND : angle 1.46274 ( 8) hydrogen bonds : bond 0.03348 ( 878) hydrogen bonds : angle 4.03152 ( 2550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.557 Fit side-chains REVERT: A 469 ASP cc_start: 0.5988 (m-30) cc_final: 0.4859 (m-30) REVERT: A 783 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 813 LYS cc_start: 0.5964 (mtpp) cc_final: 0.4908 (tttt) REVERT: B 483 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7985 (tt) REVERT: B 708 MET cc_start: 0.7176 (mtt) cc_final: 0.6896 (mtt) REVERT: C 469 ASP cc_start: 0.5988 (m-30) cc_final: 0.4851 (m-30) REVERT: C 783 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8065 (mt) REVERT: C 813 LYS cc_start: 0.5974 (mtpp) cc_final: 0.4906 (tttt) REVERT: D 483 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8000 (tt) REVERT: D 708 MET cc_start: 0.7171 (mtt) cc_final: 0.6906 (mtt) REVERT: I 103 ILE cc_start: 0.8290 (mt) cc_final: 0.8005 (mt) REVERT: I 227 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7656 (mp) REVERT: J 42 ASP cc_start: 0.6883 (p0) cc_final: 0.6682 (p0) REVERT: J 103 ILE cc_start: 0.8459 (mt) cc_final: 0.8206 (mt) outliers start: 32 outliers final: 20 residues processed: 283 average time/residue: 0.1173 time to fit residues: 50.9908 Evaluate side-chains 282 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 83 optimal weight: 0.0670 chunk 145 optimal weight: 0.5980 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.197661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169408 restraints weight = 17750.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169457 restraints weight = 37235.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.170243 restraints weight = 28493.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170622 restraints weight = 19837.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.171087 restraints weight = 19498.992| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15358 Z= 0.185 Angle : 0.572 9.521 20780 Z= 0.290 Chirality : 0.043 0.198 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.863 59.915 2518 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.42 % Allowed : 14.50 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 0.96 (0.20), residues: 1926 helix: 2.04 (0.16), residues: 1072 sheet: -2.14 (0.38), residues: 150 loop : -0.94 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 48 TYR 0.038 0.002 TYR A 707 PHE 0.012 0.002 PHE D 515 TRP 0.008 0.001 TRP C 762 HIS 0.008 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00449 (15354) covalent geometry : angle 0.57224 (20772) SS BOND : bond 0.00277 ( 4) SS BOND : angle 0.90786 ( 8) hydrogen bonds : bond 0.03658 ( 878) hydrogen bonds : angle 4.15927 ( 2550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.570 Fit side-chains REVERT: A 469 ASP cc_start: 0.5826 (m-30) cc_final: 0.4695 (m-30) REVERT: B 483 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8079 (tt) REVERT: C 469 ASP cc_start: 0.5876 (m-30) cc_final: 0.4703 (m-30) REVERT: D 483 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8182 (tt) REVERT: I 103 ILE cc_start: 0.8357 (mt) cc_final: 0.8032 (mt) REVERT: I 227 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7755 (mp) REVERT: J 42 ASP cc_start: 0.6915 (p0) cc_final: 0.6666 (p0) REVERT: J 103 ILE cc_start: 0.8359 (mt) cc_final: 0.8002 (mt) outliers start: 35 outliers final: 25 residues processed: 279 average time/residue: 0.1110 time to fit residues: 47.9453 Evaluate side-chains 285 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 185 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 chunk 41 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.211506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.182059 restraints weight = 18139.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182606 restraints weight = 37487.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183436 restraints weight = 30202.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.184968 restraints weight = 20318.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185157 restraints weight = 17639.135| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15358 Z= 0.116 Angle : 0.516 9.558 20780 Z= 0.264 Chirality : 0.041 0.172 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.212 58.931 2518 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.62 % Allowed : 15.54 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.19 (0.20), residues: 1926 helix: 2.20 (0.16), residues: 1076 sheet: -1.76 (0.38), residues: 138 loop : -0.91 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 48 TYR 0.041 0.001 TYR A 707 PHE 0.016 0.001 PHE D 491 TRP 0.009 0.001 TRP I 203 HIS 0.009 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00266 (15354) covalent geometry : angle 0.51570 (20772) SS BOND : bond 0.00285 ( 4) SS BOND : angle 0.77635 ( 8) hydrogen bonds : bond 0.03206 ( 878) hydrogen bonds : angle 4.00525 ( 2550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.428 Fit side-chains REVERT: A 469 ASP cc_start: 0.5822 (m-30) cc_final: 0.5211 (m-30) REVERT: A 813 LYS cc_start: 0.5803 (mtpp) cc_final: 0.4858 (tttt) REVERT: B 442 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 807 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (mtm) REVERT: C 469 ASP cc_start: 0.5815 (m-30) cc_final: 0.4668 (m-30) REVERT: C 707 TYR cc_start: 0.7535 (t80) cc_final: 0.7097 (t80) REVERT: C 813 LYS cc_start: 0.5888 (mtpp) cc_final: 0.4904 (tttt) REVERT: I 103 ILE cc_start: 0.8325 (mt) cc_final: 0.8045 (mt) REVERT: I 227 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7742 (mp) REVERT: J 103 ILE cc_start: 0.8349 (mt) cc_final: 0.8005 (mt) outliers start: 38 outliers final: 23 residues processed: 303 average time/residue: 0.1127 time to fit residues: 52.7376 Evaluate side-chains 297 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 807 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 151 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN I 104 ASN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.211037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181762 restraints weight = 18331.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181724 restraints weight = 36789.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182641 restraints weight = 31351.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184391 restraints weight = 20584.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184515 restraints weight = 18179.063| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15358 Z= 0.125 Angle : 0.528 10.253 20780 Z= 0.268 Chirality : 0.041 0.165 2394 Planarity : 0.004 0.054 2544 Dihedral : 9.904 59.996 2518 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 16.37 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.24 (0.20), residues: 1926 helix: 2.24 (0.16), residues: 1074 sheet: -1.76 (0.38), residues: 140 loop : -0.87 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 711 TYR 0.029 0.002 TYR A 707 PHE 0.016 0.001 PHE B 515 TRP 0.008 0.001 TRP J 203 HIS 0.008 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00290 (15354) covalent geometry : angle 0.52750 (20772) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.71571 ( 8) hydrogen bonds : bond 0.03245 ( 878) hydrogen bonds : angle 4.01463 ( 2550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.576 Fit side-chains REVERT: A 469 ASP cc_start: 0.5810 (m-30) cc_final: 0.5232 (m-30) REVERT: A 711 ARG cc_start: 0.2762 (mmp-170) cc_final: 0.2424 (mmp-170) REVERT: A 813 LYS cc_start: 0.5920 (mtpp) cc_final: 0.5020 (tttt) REVERT: B 442 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6805 (mp) REVERT: B 469 TYR cc_start: 0.6559 (m-10) cc_final: 0.6303 (m-10) REVERT: C 469 ASP cc_start: 0.5810 (m-30) cc_final: 0.5204 (m-30) REVERT: C 813 LYS cc_start: 0.6100 (mtpp) cc_final: 0.5204 (tttt) REVERT: D 469 TYR cc_start: 0.6646 (m-10) cc_final: 0.6370 (m-10) REVERT: I 103 ILE cc_start: 0.8247 (mt) cc_final: 0.7875 (mt) REVERT: I 227 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7759 (mp) REVERT: J 103 ILE cc_start: 0.8351 (mt) cc_final: 0.7941 (tt) outliers start: 35 outliers final: 30 residues processed: 296 average time/residue: 0.1157 time to fit residues: 52.5067 Evaluate side-chains 294 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.0770 chunk 97 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN I 105 HIS J 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.210580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181988 restraints weight = 18333.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.181561 restraints weight = 37310.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182480 restraints weight = 32026.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184291 restraints weight = 21020.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184350 restraints weight = 18330.497| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15358 Z= 0.130 Angle : 0.543 8.935 20780 Z= 0.275 Chirality : 0.041 0.165 2394 Planarity : 0.004 0.048 2544 Dihedral : 9.751 59.291 2518 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.56 % Allowed : 17.06 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.26 (0.20), residues: 1926 helix: 2.22 (0.16), residues: 1074 sheet: -1.51 (0.40), residues: 132 loop : -0.87 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 48 TYR 0.047 0.002 TYR A 707 PHE 0.021 0.001 PHE D 491 TRP 0.008 0.001 TRP J 203 HIS 0.008 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00306 (15354) covalent geometry : angle 0.54238 (20772) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.86106 ( 8) hydrogen bonds : bond 0.03245 ( 878) hydrogen bonds : angle 4.04421 ( 2550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.481 Fit side-chains REVERT: A 469 ASP cc_start: 0.5809 (m-30) cc_final: 0.5233 (m-30) REVERT: A 813 LYS cc_start: 0.6036 (mtpp) cc_final: 0.5153 (tttt) REVERT: B 442 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6702 (mp) REVERT: B 484 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8286 (m) REVERT: C 469 ASP cc_start: 0.5760 (m-30) cc_final: 0.5172 (m-30) REVERT: C 813 LYS cc_start: 0.6047 (mtpp) cc_final: 0.5189 (tttt) REVERT: D 469 TYR cc_start: 0.6653 (m-10) cc_final: 0.6343 (m-10) REVERT: I 103 ILE cc_start: 0.8290 (mt) cc_final: 0.7933 (mt) REVERT: I 227 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7789 (mp) REVERT: J 103 ILE cc_start: 0.8362 (mt) cc_final: 0.7980 (mt) outliers start: 37 outliers final: 31 residues processed: 292 average time/residue: 0.1107 time to fit residues: 49.8728 Evaluate side-chains 298 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN I 104 ASN I 105 HIS J 104 ASN J 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.209104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178765 restraints weight = 18250.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.178293 restraints weight = 35199.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.179574 restraints weight = 29367.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.181513 restraints weight = 20679.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181819 restraints weight = 20823.760| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15358 Z= 0.157 Angle : 0.564 10.288 20780 Z= 0.286 Chirality : 0.042 0.168 2394 Planarity : 0.004 0.058 2544 Dihedral : 9.812 59.696 2518 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.62 % Allowed : 16.92 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.15 (0.20), residues: 1926 helix: 2.15 (0.16), residues: 1072 sheet: -1.93 (0.37), residues: 164 loop : -0.76 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.038 0.002 TYR C 707 PHE 0.025 0.001 PHE D 491 TRP 0.007 0.001 TRP J 203 HIS 0.020 0.002 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00378 (15354) covalent geometry : angle 0.56386 (20772) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.93295 ( 8) hydrogen bonds : bond 0.03426 ( 878) hydrogen bonds : angle 4.12262 ( 2550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.567 Fit side-chains REVERT: A 469 ASP cc_start: 0.5904 (m-30) cc_final: 0.5334 (m-30) REVERT: A 711 ARG cc_start: 0.2731 (mmp-170) cc_final: 0.2431 (mmp-170) REVERT: A 813 LYS cc_start: 0.6064 (mtpp) cc_final: 0.5124 (tttt) REVERT: B 442 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6579 (mp) REVERT: C 469 ASP cc_start: 0.5941 (m-30) cc_final: 0.5364 (m-30) REVERT: C 813 LYS cc_start: 0.6138 (mtpp) cc_final: 0.5187 (tttt) REVERT: I 198 HIS cc_start: 0.7055 (t-90) cc_final: 0.6807 (t-170) REVERT: I 227 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7823 (mp) REVERT: J 103 ILE cc_start: 0.8355 (mt) cc_final: 0.7912 (tt) outliers start: 38 outliers final: 33 residues processed: 279 average time/residue: 0.1109 time to fit residues: 47.4074 Evaluate side-chains 298 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 175 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN I 104 ASN I 105 HIS J 104 ASN J 198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.210290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.181864 restraints weight = 18251.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181631 restraints weight = 37474.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182513 restraints weight = 31302.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183994 restraints weight = 20827.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.184119 restraints weight = 19214.894| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15358 Z= 0.135 Angle : 0.561 10.432 20780 Z= 0.284 Chirality : 0.041 0.167 2394 Planarity : 0.004 0.057 2544 Dihedral : 9.576 57.474 2518 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.49 % Allowed : 17.47 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 are not related in a simple way. whole: 1.20 (0.20), residues: 1926 helix: 2.20 (0.16), residues: 1072 sheet: -1.92 (0.37), residues: 164 loop : -0.75 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 48 TYR 0.054 0.002 TYR A 707 PHE 0.030 0.001 PHE D 491 TRP 0.009 0.001 TRP I 203 HIS 0.011 0.002 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00319 (15354) covalent geometry : angle 0.56043 (20772) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.93157 ( 8) hydrogen bonds : bond 0.03316 ( 878) hydrogen bonds : angle 4.10994 ( 2550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.81 seconds wall clock time: 40 minutes 25.10 seconds (2425.10 seconds total)