Starting phenix.real_space_refine on Fri Jun 13 22:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhb_13969/06_2025/7qhb_13969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhb_13969/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qhb_13969/06_2025/7qhb_13969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhb_13969/06_2025/7qhb_13969.map" model { file = "/net/cci-nas-00/data/ceres_data/7qhb_13969/06_2025/7qhb_13969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhb_13969/06_2025/7qhb_13969.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} 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: {'TYR:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} 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: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} 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: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} 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: 11.96, per 1000 atoms: 0.79 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: 4.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.49 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: 4.89 Time building geometry restraints manager: 4.84 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 or resid 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 or resid 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: 3.260 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.500 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), 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 TRP 0.010 0.002 TRP B 605 HIS 0.007 0.002 HIS J 83 PHE 0.023 0.003 PHE D 541 TYR 0.039 0.003 TYR B 700 ARG 0.027 0.001 ARG J 122 Details of bonding type rmsd hydrogen bonds : bond 0.14113 ( 878) hydrogen bonds : angle 6.93624 ( 2550) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.80312 ( 8) covalent geometry : bond 0.01755 (15354) covalent geometry : angle 1.04990 (20772) *********************** 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 : 1.590 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: 0.2525 time to fit residues: 108.1799 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 : 1.745 ------------------------------------------------------------------------------- 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 162 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.208748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180568 restraints weight = 18171.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180136 restraints weight = 35002.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.181234 restraints weight = 28051.787| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15358 Z= 0.157 Angle : 0.606 9.426 20780 Z= 0.312 Chirality : 0.044 0.206 2394 Planarity : 0.005 0.045 2544 Dihedral : 13.404 101.252 2518 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1926 helix: 1.69 (0.16), residues: 1070 sheet: -2.75 (0.37), residues: 146 loop : -1.56 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 605 HIS 0.013 0.002 HIS J 83 PHE 0.010 0.001 PHE C 542 TYR 0.017 0.002 TYR C 401 ARG 0.006 0.001 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 878) hydrogen bonds : angle 4.44052 ( 2550) SS BOND : bond 0.00443 ( 4) SS BOND : angle 0.58617 ( 8) covalent geometry : bond 0.00353 (15354) covalent geometry : angle 0.60608 (20772) *********************** 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 298 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 282 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8330 (mm) cc_final: 0.7936 (pt) REVERT: A 711 ARG cc_start: 0.3349 (mmp-170) cc_final: 0.3038 (mmp80) REVERT: A 812 TYR cc_start: 0.6384 (t80) cc_final: 0.6150 (t80) REVERT: A 813 LYS cc_start: 0.6155 (mtpp) cc_final: 0.5295 (tttt) REVERT: B 642 GLN cc_start: 0.7473 (pp30) cc_final: 0.6988 (pp30) REVERT: B 674 MET cc_start: 0.7349 (ptm) cc_final: 0.7085 (ptm) REVERT: B 766 TRP cc_start: 0.5835 (m100) cc_final: 0.5498 (m100) REVERT: C 496 ILE cc_start: 0.8339 (mm) cc_final: 0.7947 (pt) REVERT: C 812 TYR cc_start: 0.6402 (t80) cc_final: 0.6158 (t80) REVERT: C 813 LYS cc_start: 0.6134 (mtpp) cc_final: 0.5286 (tttt) REVERT: D 642 GLN cc_start: 0.7478 (pp30) cc_final: 0.6991 (pp30) REVERT: D 674 MET cc_start: 0.7327 (ptm) cc_final: 0.7120 (ptm) REVERT: D 766 TRP cc_start: 0.5858 (m100) cc_final: 0.5521 (m100) REVERT: I 42 ASP cc_start: 0.7359 (p0) cc_final: 0.6348 (p0) REVERT: J 42 ASP cc_start: 0.7276 (p0) cc_final: 0.6224 (p0) outliers start: 16 outliers final: 6 residues processed: 286 average time/residue: 0.2812 time to fit residues: 119.4182 Evaluate side-chains 251 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 245 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 174 optimal weight: 0.0570 chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.207810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.178041 restraints weight = 18175.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177254 restraints weight = 34944.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.178593 restraints weight = 29582.979| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2680 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= 0.131 Angle : 0.535 8.891 20780 Z= 0.274 Chirality : 0.041 0.153 2394 Planarity : 0.004 0.040 2544 Dihedral : 12.230 92.112 2518 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.07 % Allowed : 11.60 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1926 helix: 2.16 (0.16), residues: 1072 sheet: -2.34 (0.36), residues: 154 loop : -1.18 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 460 HIS 0.010 0.001 HIS I 83 PHE 0.011 0.001 PHE B 515 TYR 0.017 0.001 TYR C 401 ARG 0.005 0.000 ARG C 657 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 878) hydrogen bonds : angle 4.12973 ( 2550) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.66170 ( 8) covalent geometry : bond 0.00306 (15354) covalent geometry : angle 0.53462 (20772) *********************** 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: 30 poor density : 274 time to evaluate : 1.673 Fit side-chains REVERT: A 469 ASP cc_start: 0.5439 (m-30) cc_final: 0.4417 (m-30) REVERT: A 812 TYR cc_start: 0.6452 (t80) cc_final: 0.6248 (t80) REVERT: B 642 GLN cc_start: 0.7437 (pp30) cc_final: 0.7012 (pp30) REVERT: B 674 MET cc_start: 0.7465 (ptm) cc_final: 0.7264 (ptm) REVERT: B 708 MET cc_start: 0.7154 (mtt) cc_final: 0.6861 (mtt) REVERT: C 469 ASP cc_start: 0.5427 (m-30) cc_final: 0.4397 (m-30) REVERT: C 717 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.7058 (ttp) REVERT: C 812 TYR cc_start: 0.6444 (t80) cc_final: 0.6229 (t80) REVERT: D 642 GLN cc_start: 0.7410 (pp30) cc_final: 0.6971 (pp30) REVERT: D 674 MET cc_start: 0.7423 (ptm) cc_final: 0.7223 (ptm) REVERT: D 708 MET cc_start: 0.7151 (mtt) cc_final: 0.6867 (mtt) REVERT: D 807 MET cc_start: 0.8476 (mtm) cc_final: 0.8250 (mtm) REVERT: I 227 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7624 (mp) outliers start: 30 outliers final: 15 residues processed: 284 average time/residue: 0.2599 time to fit residues: 110.4529 Evaluate side-chains 273 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE 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 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 717 MET 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 91 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4287 r_free = 0.4287 target = 0.204559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.176110 restraints weight = 18143.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175929 restraints weight = 24281.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.168843 restraints weight = 21431.139| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3118 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= 0.162 Angle : 0.555 6.581 20780 Z= 0.285 Chirality : 0.041 0.147 2394 Planarity : 0.004 0.043 2544 Dihedral : 11.632 80.083 2518 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 12.85 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1926 helix: 2.14 (0.16), residues: 1072 sheet: -2.19 (0.37), residues: 148 loop : -1.04 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 762 HIS 0.009 0.001 HIS I 83 PHE 0.013 0.001 PHE D 515 TYR 0.018 0.002 TYR C 401 ARG 0.005 0.000 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 878) hydrogen bonds : angle 4.13705 ( 2550) SS BOND : bond 0.00666 ( 4) SS BOND : angle 0.61653 ( 8) covalent geometry : bond 0.00389 (15354) covalent geometry : angle 0.55521 (20772) *********************** 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 308 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 469 ASP cc_start: 0.5680 (m-30) cc_final: 0.4612 (m-30) REVERT: A 492 MET cc_start: 0.7934 (ttm) cc_final: 0.7725 (ttm) REVERT: A 813 LYS cc_start: 0.5845 (mtpp) cc_final: 0.4866 (tttt) REVERT: B 483 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 642 GLN cc_start: 0.7533 (pp30) cc_final: 0.7072 (pp30) REVERT: B 708 MET cc_start: 0.7210 (mtt) cc_final: 0.6943 (mtt) REVERT: C 469 ASP cc_start: 0.5688 (m-30) cc_final: 0.4625 (m-30) REVERT: C 477 ILE cc_start: 0.7885 (mp) cc_final: 0.7683 (mp) REVERT: C 717 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.7003 (ttp) REVERT: C 813 LYS cc_start: 0.5773 (mtpp) cc_final: 0.4847 (tttt) REVERT: D 483 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8041 (tt) REVERT: D 642 GLN cc_start: 0.7535 (pp30) cc_final: 0.7071 (pp30) REVERT: D 708 MET cc_start: 0.7216 (mtt) cc_final: 0.6942 (mtt) REVERT: I 42 ASP cc_start: 0.6867 (p0) cc_final: 0.6646 (p0) REVERT: I 103 ILE cc_start: 0.8239 (mt) cc_final: 0.7971 (mt) REVERT: I 227 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7559 (mp) REVERT: J 42 ASP cc_start: 0.6894 (p0) cc_final: 0.6687 (p0) REVERT: J 48 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6972 (ttm-80) outliers start: 28 outliers final: 14 residues processed: 288 average time/residue: 0.2507 time to fit residues: 109.4480 Evaluate side-chains 281 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 717 MET 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 65 optimal weight: 0.0870 chunk 181 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 104 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.204911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172152 restraints weight = 18239.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163442 restraints weight = 27171.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161872 restraints weight = 29946.477| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3358 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= 0.139 Angle : 0.546 9.980 20780 Z= 0.275 Chirality : 0.041 0.196 2394 Planarity : 0.004 0.040 2544 Dihedral : 10.948 63.907 2518 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.14 % Allowed : 13.88 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1926 helix: 2.17 (0.16), residues: 1074 sheet: -2.08 (0.36), residues: 156 loop : -0.87 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 605 HIS 0.009 0.001 HIS J 83 PHE 0.014 0.001 PHE D 515 TYR 0.025 0.001 TYR C 707 ARG 0.004 0.000 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 878) hydrogen bonds : angle 4.06866 ( 2550) SS BOND : bond 0.00120 ( 4) SS BOND : angle 1.64323 ( 8) covalent geometry : bond 0.00328 (15354) covalent geometry : angle 0.54487 (20772) *********************** 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 293 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 262 time to evaluate : 1.542 Fit side-chains REVERT: A 469 ASP cc_start: 0.6208 (m-30) cc_final: 0.5057 (m-30) REVERT: A 813 LYS cc_start: 0.5985 (mtpp) cc_final: 0.4825 (tttt) REVERT: B 483 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8054 (tt) REVERT: B 708 MET cc_start: 0.7238 (mtt) cc_final: 0.6949 (mtt) REVERT: C 469 ASP cc_start: 0.6348 (m-30) cc_final: 0.5178 (m-30) REVERT: C 717 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7102 (ttp) REVERT: C 813 LYS cc_start: 0.6071 (mtpp) cc_final: 0.4990 (tttt) REVERT: D 483 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8058 (tt) REVERT: D 708 MET cc_start: 0.7240 (mtt) cc_final: 0.6953 (mtt) REVERT: I 35 MET cc_start: 0.7482 (tpt) cc_final: 0.7241 (tpt) REVERT: I 42 ASP cc_start: 0.6983 (p0) cc_final: 0.6690 (p0) REVERT: I 227 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7443 (mp) REVERT: J 42 ASP cc_start: 0.7005 (p0) cc_final: 0.6701 (p0) outliers start: 31 outliers final: 18 residues processed: 278 average time/residue: 0.2914 time to fit residues: 121.4810 Evaluate side-chains 276 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 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 717 MET Chi-restraints excluded: chain C residue 742 VAL 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 227 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 100 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 104 ASN I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.203983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.171770 restraints weight = 18166.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169813 restraints weight = 33264.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170750 restraints weight = 32027.583| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15358 Z= 0.266 Angle : 0.666 9.281 20780 Z= 0.334 Chirality : 0.045 0.207 2394 Planarity : 0.004 0.043 2544 Dihedral : 11.608 61.224 2518 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.04 % Allowed : 14.23 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1926 helix: 1.75 (0.16), residues: 1070 sheet: -2.41 (0.33), residues: 184 loop : -1.05 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 601 HIS 0.007 0.001 HIS J 83 PHE 0.017 0.002 PHE I 29 TYR 0.048 0.002 TYR A 707 ARG 0.007 0.001 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 878) hydrogen bonds : angle 4.39472 ( 2550) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.92695 ( 8) covalent geometry : bond 0.00651 (15354) covalent geometry : angle 0.66544 (20772) *********************** 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 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.493 Fit side-chains REVERT: A 469 ASP cc_start: 0.5900 (m-30) cc_final: 0.4780 (m-30) REVERT: B 442 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7123 (mp) REVERT: B 483 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8337 (tt) REVERT: C 469 ASP cc_start: 0.6023 (m-30) cc_final: 0.4840 (m-30) REVERT: C 711 ARG cc_start: 0.3479 (mmp-170) cc_final: 0.3032 (mmp-170) REVERT: D 483 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8308 (tt) REVERT: I 42 ASP cc_start: 0.6923 (p0) cc_final: 0.6662 (p0) REVERT: I 48 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6604 (ttm-80) REVERT: I 103 ILE cc_start: 0.8321 (mt) cc_final: 0.8040 (tt) REVERT: I 227 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7778 (mp) REVERT: J 42 ASP cc_start: 0.6928 (p0) cc_final: 0.6697 (p0) REVERT: J 103 ILE cc_start: 0.8136 (mt) cc_final: 0.7902 (tt) outliers start: 44 outliers final: 32 residues processed: 277 average time/residue: 0.2489 time to fit residues: 104.9777 Evaluate side-chains 276 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 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 708 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 483 LEU Chi-restraints excluded: chain D residue 484 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 0.3980 chunk 185 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 162 optimal weight: 0.0870 chunk 190 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 0.0060 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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** ** 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 = 0.4340 r_free = 0.4340 target = 0.210832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181944 restraints weight = 18295.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182003 restraints weight = 37113.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183155 restraints weight = 28760.810| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15358 Z= 0.110 Angle : 0.523 9.432 20780 Z= 0.267 Chirality : 0.041 0.188 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.565 58.604 2518 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.62 % Allowed : 15.33 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 1926 helix: 2.18 (0.16), residues: 1074 sheet: -2.13 (0.36), residues: 156 loop : -0.86 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 203 HIS 0.010 0.001 HIS I 83 PHE 0.012 0.001 PHE D 515 TYR 0.043 0.002 TYR A 707 ARG 0.006 0.000 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 878) hydrogen bonds : angle 4.06747 ( 2550) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.66446 ( 8) covalent geometry : bond 0.00246 (15354) covalent geometry : angle 0.52278 (20772) *********************** 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 294 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 1.471 Fit side-chains REVERT: A 469 ASP cc_start: 0.5799 (m-30) cc_final: 0.4652 (m-30) REVERT: A 641 ILE cc_start: 0.4760 (mp) cc_final: 0.4487 (mt) REVERT: B 483 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8263 (tt) REVERT: C 469 ASP cc_start: 0.5825 (m-30) cc_final: 0.4668 (m-30) REVERT: C 711 ARG cc_start: 0.3263 (mmp-170) cc_final: 0.2715 (mmp-170) REVERT: D 483 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8261 (tt) REVERT: I 227 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7847 (mp) REVERT: J 103 ILE cc_start: 0.8183 (mt) cc_final: 0.7968 (tt) outliers start: 38 outliers final: 27 residues processed: 273 average time/residue: 0.2433 time to fit residues: 100.9732 Evaluate side-chains 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 708 ILE Chi-restraints excluded: chain A residue 742 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 625 THR 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 D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 751 LEU 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 82 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 104 ASN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.209749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181271 restraints weight = 18194.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180830 restraints weight = 36566.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182121 restraints weight = 28591.145| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3941 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= 0.131 Angle : 0.531 8.991 20780 Z= 0.272 Chirality : 0.041 0.185 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.128 59.695 2518 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.49 % Allowed : 16.64 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1926 helix: 2.16 (0.16), residues: 1074 sheet: -2.06 (0.37), residues: 152 loop : -0.86 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 203 HIS 0.009 0.001 HIS I 83 PHE 0.011 0.001 PHE D 515 TYR 0.043 0.001 TYR C 707 ARG 0.007 0.000 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 878) hydrogen bonds : angle 4.07075 ( 2550) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.84321 ( 8) covalent geometry : bond 0.00306 (15354) covalent geometry : angle 0.53114 (20772) *********************** 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 309 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 1.554 Fit side-chains REVERT: A 469 ASP cc_start: 0.5860 (m-30) cc_final: 0.4655 (m-30) REVERT: A 641 ILE cc_start: 0.4723 (mp) cc_final: 0.4458 (mt) REVERT: A 710 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6323 (mm-40) REVERT: A 711 ARG cc_start: 0.3466 (mmp80) cc_final: 0.2941 (mmp-170) REVERT: A 813 LYS cc_start: 0.6148 (mtpp) cc_final: 0.5048 (tttt) REVERT: B 483 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 469 ASP cc_start: 0.5862 (m-30) cc_final: 0.4656 (m-30) REVERT: C 813 LYS cc_start: 0.6057 (mtpp) cc_final: 0.4966 (tttt) REVERT: D 483 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (tt) REVERT: I 48 ARG cc_start: 0.7035 (ttm-80) cc_final: 0.6735 (ttm110) REVERT: I 227 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7845 (mp) REVERT: J 103 ILE cc_start: 0.8194 (mt) cc_final: 0.7943 (tt) outliers start: 36 outliers final: 27 residues processed: 290 average time/residue: 0.2506 time to fit residues: 110.6264 Evaluate side-chains 296 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 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 625 THR 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 D residue 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 751 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 0.0370 chunk 107 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 139 optimal weight: 0.1980 chunk 136 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 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 = 0.4335 r_free = 0.4335 target = 0.210349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.181366 restraints weight = 18183.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181527 restraints weight = 36525.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182467 restraints weight = 31617.480| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4071 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 : 0.545 10.090 20780 Z= 0.273 Chirality : 0.041 0.168 2394 Planarity : 0.004 0.044 2544 Dihedral : 9.689 59.940 2518 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.35 % Allowed : 16.57 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1926 helix: 2.19 (0.16), residues: 1074 sheet: -2.02 (0.38), residues: 152 loop : -0.89 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 203 HIS 0.009 0.002 HIS I 83 PHE 0.019 0.001 PHE B 515 TYR 0.043 0.002 TYR A 707 ARG 0.007 0.000 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 878) hydrogen bonds : angle 4.05043 ( 2550) SS BOND : bond 0.00190 ( 4) SS BOND : angle 0.78848 ( 8) covalent geometry : bond 0.00291 (15354) covalent geometry : angle 0.54507 (20772) *********************** 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 314 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 1.638 Fit side-chains REVERT: A 469 ASP cc_start: 0.5823 (m-30) cc_final: 0.4581 (m-30) REVERT: A 641 ILE cc_start: 0.4583 (mp) cc_final: 0.4332 (mt) REVERT: A 813 LYS cc_start: 0.5981 (mtpp) cc_final: 0.4987 (tttt) REVERT: B 483 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8288 (tt) REVERT: C 469 ASP cc_start: 0.5800 (m-30) cc_final: 0.4551 (m-30) REVERT: C 711 ARG cc_start: 0.3278 (mmp-170) cc_final: 0.2791 (mmp-170) REVERT: C 813 LYS cc_start: 0.6038 (mtpp) cc_final: 0.5119 (tttt) REVERT: I 48 ARG cc_start: 0.7006 (ttm-80) cc_final: 0.6739 (ttm110) REVERT: I 227 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7849 (mp) REVERT: J 103 ILE cc_start: 0.8169 (mt) cc_final: 0.7968 (tt) outliers start: 34 outliers final: 27 residues processed: 294 average time/residue: 0.2894 time to fit residues: 127.4599 Evaluate side-chains 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 625 THR 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 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 D residue 407 MET Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 751 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 198 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 = 0.4291 r_free = 0.4291 target = 0.205674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173821 restraints weight = 18174.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.174172 restraints weight = 28880.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.174878 restraints weight = 25636.966| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15358 Z= 0.204 Angle : 0.611 9.802 20780 Z= 0.308 Chirality : 0.043 0.182 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.075 59.994 2518 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.07 % Allowed : 17.33 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1926 helix: 1.96 (0.16), residues: 1074 sheet: -2.04 (0.36), residues: 174 loop : -0.91 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 203 HIS 0.008 0.001 HIS I 83 PHE 0.013 0.002 PHE B 515 TYR 0.045 0.002 TYR C 707 ARG 0.007 0.000 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 878) hydrogen bonds : angle 4.26388 ( 2550) SS BOND : bond 0.00172 ( 4) SS BOND : angle 1.01711 ( 8) covalent geometry : bond 0.00498 (15354) covalent geometry : angle 0.61076 (20772) ********************** 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 279 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 1.701 Fit side-chains REVERT: A 469 ASP cc_start: 0.5970 (m-30) cc_final: 0.4671 (m-30) REVERT: B 483 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 469 ASP cc_start: 0.6008 (m-30) cc_final: 0.5336 (m-30) REVERT: C 711 ARG cc_start: 0.3459 (mmp-170) cc_final: 0.3206 (mmp-170) REVERT: I 48 ARG cc_start: 0.7009 (ttm-80) cc_final: 0.6792 (ttm110) REVERT: I 227 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7894 (mp) REVERT: J 48 ARG cc_start: 0.6970 (ttm110) cc_final: 0.6671 (ttm-80) outliers start: 30 outliers final: 25 residues processed: 263 average time/residue: 0.2510 time to fit residues: 100.3812 Evaluate side-chains 271 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 742 VAL 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 625 THR 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 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 D residue 407 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 198 HIS Chi-restraints excluded: chain I residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 135 optimal weight: 0.0060 chunk 147 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 198 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 = 0.4329 r_free = 0.4329 target = 0.209775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.180652 restraints weight = 18334.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.179530 restraints weight = 35463.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.180933 restraints weight = 29996.039| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15358 Z= 0.125 Angle : 0.560 10.392 20780 Z= 0.282 Chirality : 0.041 0.166 2394 Planarity : 0.004 0.044 2544 Dihedral : 9.589 59.806 2518 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.07 % Allowed : 17.20 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1926 helix: 2.13 (0.16), residues: 1074 sheet: -1.88 (0.36), residues: 176 loop : -0.86 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 203 HIS 0.010 0.001 HIS I 83 PHE 0.013 0.001 PHE D 491 TYR 0.030 0.002 TYR A 707 ARG 0.007 0.000 ARG I 48 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 878) hydrogen bonds : angle 4.15822 ( 2550) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.86651 ( 8) covalent geometry : bond 0.00292 (15354) covalent geometry : angle 0.55960 (20772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4654.11 seconds wall clock time: 82 minutes 25.12 seconds (4945.12 seconds total)