Starting phenix.real_space_refine on Thu Feb 5 05:30:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qhb_13969/02_2026/7qhb_13969.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qhb_13969/02_2026/7qhb_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_13969/02_2026/7qhb_13969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qhb_13969/02_2026/7qhb_13969.map" model { file = "/net/cci-nas-00/data/ceres_data/7qhb_13969/02_2026/7qhb_13969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qhb_13969/02_2026/7qhb_13969.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 94 5.16 5 Cl 4 4.86 5 C 9886 2.51 5 N 2374 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15052 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 13, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'TYR:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 13, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'TYR:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 78 Chain: "I" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {'79N': 1, 'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU A1202 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {'79N': 2, 'CYZ': 1, 'PAM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU C1202 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Unusual residues: {'79N': 1, 'CYZ': 1, 'PAM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 3.86, per 1000 atoms: 0.26 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=8, 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 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 722.9 milliseconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 24 sheets defined 56.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.639A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 681 through 691 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 789 through 815 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.718A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.722A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 4.040A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 582 removed outlier: 3.640A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 621 removed outlier: 3.828A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.540A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 789 through 815 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 removed outlier: 4.881A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.717A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.957A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.571A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 151 Processing helix chain 'I' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 40 removed outlier: 3.698A pdb=" N LEU J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 128 removed outlier: 3.823A pdb=" N LEU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 151 Processing helix chain 'J' and resid 155 through 184 removed outlier: 3.828A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 234 removed outlier: 3.569A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 439 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 439 through 444 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 436 through 440 removed outlier: 6.156A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU C 439 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 487 Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB7, first strand: chain 'C' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 439 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.905A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.985A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 45 through 49 removed outlier: 3.867A pdb=" N HIS I 83 " --> pdb=" O CYS I 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 45 through 49 removed outlier: 3.868A pdb=" N HIS J 83 " --> pdb=" O CYS J 90 " (cutoff:3.500A) 886 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 2.05 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: 473 49.45 - 74.18: 78 74.18 - 98.90: 18 98.90 - 123.63: 20 Dihedral angle restraints: 9046 sinusoidal: 3432 harmonic: 5614 Sorted by residual: dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual 93.00 133.51 -40.51 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual 93.00 133.50 -40.50 1 1.00e+01 1.00e-02 2.30e+01 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 ... (remaining 9043 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: 2.14 - 2.70: 616 2.70 - 3.25: 16600 3.25 - 3.80: 24699 3.80 - 4.35: 30431 4.35 - 4.90: 52546 Nonbonded interactions: 124892 Sorted by model distance: nonbonded pdb=" O1 79N D 903 " pdb=" O3 79N D 903 " model vdw 2.144 3.040 nonbonded pdb=" O1 79N B 903 " pdb=" O3 79N B 903 " model vdw 2.144 3.040 nonbonded pdb=" O THR I 110 " pdb=" OD1 ASP I 111 " model vdw 2.187 3.040 nonbonded pdb=" O THR J 110 " pdb=" OD1 ASP J 111 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR A 651 " pdb=" OE2 GLU A1202 " model vdw 2.214 3.040 ... (remaining 124887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'B' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) selection = (chain 'C' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'D' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.660 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 15362 Z= 0.701 Angle : 1.051 13.568 20788 Z= 0.536 Chirality : 0.068 0.420 2394 Planarity : 0.005 0.058 2544 Dihedral : 17.095 123.629 5438 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.55 % Allowed : 0.69 % Favored : 98.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 1926 helix: -0.28 (0.15), residues: 1056 sheet: -2.63 (0.35), residues: 172 loop : -2.55 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG J 122 TYR 0.039 0.003 TYR B 700 PHE 0.023 0.003 PHE D 541 TRP 0.010 0.002 TRP B 605 HIS 0.007 0.002 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.01755 (15354) covalent geometry : angle 1.04990 (20772) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.79979 ( 16) hydrogen bonds : bond 0.14113 ( 878) hydrogen bonds : angle 6.93624 ( 2550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 284 time to evaluate : 0.570 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: 0.1204 time to fit residues: 52.3829 Evaluate side-chains 243 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain D residue 744 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN I 105 HIS I 172 ASN ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 105 HIS ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.208429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.181071 restraints weight = 18275.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.181339 restraints weight = 38336.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183352 restraints weight = 27069.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.183085 restraints weight = 20072.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183883 restraints weight = 16801.213| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15362 Z= 0.168 Angle : 0.610 9.536 20788 Z= 0.315 Chirality : 0.044 0.199 2394 Planarity : 0.005 0.044 2544 Dihedral : 13.551 102.233 2518 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.10 % Allowed : 9.67 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1926 helix: 1.64 (0.16), residues: 1070 sheet: -2.36 (0.38), residues: 128 loop : -1.69 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 711 TYR 0.016 0.002 TYR C 401 PHE 0.011 0.001 PHE C 542 TRP 0.010 0.001 TRP B 605 HIS 0.012 0.002 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00377 (15354) covalent geometry : angle 0.60971 (20772) SS BOND : bond 0.00298 ( 8) SS BOND : angle 0.83510 ( 16) hydrogen bonds : bond 0.04000 ( 878) hydrogen bonds : angle 4.49500 ( 2550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 288 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 ILE cc_start: 0.8329 (mm) cc_final: 0.7929 (pt) REVERT: A 711 ARG cc_start: 0.3287 (mmp-170) cc_final: 0.3002 (mmp80) REVERT: A 812 TYR cc_start: 0.6428 (t80) cc_final: 0.6185 (t80) REVERT: A 813 LYS cc_start: 0.6091 (mtpp) cc_final: 0.5231 (tttt) REVERT: B 642 GLN cc_start: 0.7479 (pp30) cc_final: 0.6986 (pp30) REVERT: B 674 MET cc_start: 0.7362 (ptm) cc_final: 0.7096 (ptm) REVERT: B 766 TRP cc_start: 0.5893 (m100) cc_final: 0.5538 (m100) REVERT: C 496 ILE cc_start: 0.8338 (mm) cc_final: 0.7941 (pt) REVERT: C 711 ARG cc_start: 0.3348 (mmp-170) cc_final: 0.3114 (mmp80) REVERT: C 812 TYR cc_start: 0.6405 (t80) cc_final: 0.6153 (t80) REVERT: C 813 LYS cc_start: 0.6158 (mtpp) cc_final: 0.5324 (tttt) REVERT: D 642 GLN cc_start: 0.7483 (pp30) cc_final: 0.6989 (pp30) REVERT: D 674 MET cc_start: 0.7371 (ptm) cc_final: 0.7139 (ptm) REVERT: D 766 TRP cc_start: 0.5892 (m100) cc_final: 0.5538 (m100) REVERT: J 227 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7570 (mp) outliers start: 16 outliers final: 6 residues processed: 292 average time/residue: 0.1303 time to fit residues: 56.8014 Evaluate side-chains 254 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 247 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 141 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 149 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.207700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.183164 restraints weight = 18395.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181223 restraints weight = 35709.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178767 restraints weight = 20092.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179120 restraints weight = 19806.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179802 restraints weight = 14913.189| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15362 Z= 0.134 Angle : 0.536 8.642 20788 Z= 0.276 Chirality : 0.041 0.155 2394 Planarity : 0.004 0.041 2544 Dihedral : 12.406 93.871 2518 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.14 % Allowed : 11.67 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1926 helix: 2.13 (0.16), residues: 1072 sheet: -2.07 (0.39), residues: 126 loop : -1.34 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 657 TYR 0.016 0.001 TYR C 401 PHE 0.011 0.001 PHE I 130 TRP 0.010 0.001 TRP B 460 HIS 0.011 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00314 (15354) covalent geometry : angle 0.53579 (20772) SS BOND : bond 0.00329 ( 8) SS BOND : angle 0.79833 ( 16) hydrogen bonds : bond 0.03567 ( 878) hydrogen bonds : angle 4.16692 ( 2550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 282 time to evaluate : 0.610 Fit side-chains REVERT: A 469 ASP cc_start: 0.5485 (m-30) cc_final: 0.4444 (m-30) REVERT: A 711 ARG cc_start: 0.3406 (mmp-170) cc_final: 0.3190 (mmp80) REVERT: A 812 TYR cc_start: 0.6459 (t80) cc_final: 0.6254 (t80) REVERT: B 642 GLN cc_start: 0.7441 (pp30) cc_final: 0.6943 (pp30) REVERT: B 674 MET cc_start: 0.7447 (ptm) cc_final: 0.7235 (ptm) REVERT: C 469 ASP cc_start: 0.5454 (m-30) cc_final: 0.4414 (m-30) REVERT: C 717 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7049 (ttp) REVERT: C 812 TYR cc_start: 0.6452 (t80) cc_final: 0.6234 (t80) REVERT: D 642 GLN cc_start: 0.7439 (pp30) cc_final: 0.6943 (pp30) REVERT: I 227 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7645 (mp) REVERT: J 227 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7669 (mp) outliers start: 31 outliers final: 17 residues processed: 293 average time/residue: 0.1237 time to fit residues: 55.2369 Evaluate side-chains 277 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 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 C residue 749 LEU 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 Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 139 optimal weight: 0.0970 chunk 82 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** I 105 HIS ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.205115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175912 restraints weight = 18179.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 81)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.171024 restraints weight = 27095.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.168910 restraints weight = 26090.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.169027 restraints weight = 27641.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.169620 restraints weight = 22317.685| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15362 Z= 0.157 Angle : 0.551 6.497 20788 Z= 0.283 Chirality : 0.041 0.148 2394 Planarity : 0.004 0.042 2544 Dihedral : 11.725 83.523 2518 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.07 % Allowed : 12.78 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1926 helix: 2.17 (0.16), residues: 1070 sheet: -1.89 (0.39), residues: 128 loop : -1.17 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 739 TYR 0.016 0.001 TYR A 401 PHE 0.011 0.001 PHE B 515 TRP 0.010 0.001 TRP C 762 HIS 0.010 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00373 (15354) covalent geometry : angle 0.55123 (20772) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.77022 ( 16) hydrogen bonds : bond 0.03556 ( 878) hydrogen bonds : angle 4.13278 ( 2550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.583 Fit side-chains REVERT: A 469 ASP cc_start: 0.5758 (m-30) cc_final: 0.4677 (m-30) REVERT: A 813 LYS cc_start: 0.5723 (mtpp) cc_final: 0.4799 (tttt) REVERT: B 483 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8007 (tt) REVERT: B 642 GLN cc_start: 0.7521 (pp30) cc_final: 0.7039 (pp30) REVERT: B 708 MET cc_start: 0.7226 (mtt) cc_final: 0.6944 (mtt) REVERT: C 469 ASP cc_start: 0.5717 (m-30) cc_final: 0.4644 (m-30) REVERT: C 717 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6998 (ttp) REVERT: C 813 LYS cc_start: 0.5728 (mtpp) cc_final: 0.4812 (tttt) REVERT: D 483 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8005 (tt) REVERT: D 642 GLN cc_start: 0.7520 (pp30) cc_final: 0.7035 (pp30) REVERT: D 708 MET cc_start: 0.7226 (mtt) cc_final: 0.6940 (mtt) REVERT: I 227 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7592 (mp) REVERT: J 227 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7727 (mp) outliers start: 30 outliers final: 17 residues processed: 293 average time/residue: 0.1198 time to fit residues: 53.4281 Evaluate side-chains 284 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 407 MET Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain I residue 89 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.203808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174846 restraints weight = 18397.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.165919 restraints weight = 24906.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163857 restraints weight = 30098.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163793 restraints weight = 27317.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163478 restraints weight = 23258.384| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15362 Z= 0.167 Angle : 0.564 10.910 20788 Z= 0.284 Chirality : 0.042 0.206 2394 Planarity : 0.004 0.044 2544 Dihedral : 11.145 64.727 2518 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.62 % Allowed : 13.26 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1926 helix: 2.11 (0.16), residues: 1072 sheet: -1.86 (0.42), residues: 120 loop : -0.97 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 711 TYR 0.017 0.001 TYR A 401 PHE 0.015 0.001 PHE D 515 TRP 0.009 0.001 TRP C 762 HIS 0.009 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00400 (15354) covalent geometry : angle 0.56354 (20772) SS BOND : bond 0.00325 ( 8) SS BOND : angle 1.09802 ( 16) hydrogen bonds : bond 0.03586 ( 878) hydrogen bonds : angle 4.15658 ( 2550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 0.566 Fit side-chains REVERT: A 469 ASP cc_start: 0.5886 (m-30) cc_final: 0.4716 (m-30) REVERT: A 710 GLN cc_start: 0.6217 (mm110) cc_final: 0.6014 (mm-40) REVERT: A 711 ARG cc_start: 0.3759 (mmp-170) cc_final: 0.3219 (mmp-170) REVERT: B 708 MET cc_start: 0.7361 (mtt) cc_final: 0.7099 (mtt) REVERT: C 469 ASP cc_start: 0.5975 (m-30) cc_final: 0.4759 (m-30) REVERT: D 442 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6935 (mp) REVERT: D 708 MET cc_start: 0.7358 (mtt) cc_final: 0.7109 (mtt) REVERT: I 35 MET cc_start: 0.7432 (tpt) cc_final: 0.7139 (tpt) REVERT: I 227 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 38 outliers final: 21 residues processed: 285 average time/residue: 0.1255 time to fit residues: 53.8715 Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 257 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 442 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 89 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 83 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 156 optimal weight: 0.0020 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.195757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161150 restraints weight = 18245.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.149406 restraints weight = 26863.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147102 restraints weight = 31640.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147940 restraints weight = 28637.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148179 restraints weight = 22849.020| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15362 Z= 0.239 Angle : 0.623 9.385 20788 Z= 0.316 Chirality : 0.044 0.203 2394 Planarity : 0.004 0.044 2544 Dihedral : 11.326 60.544 2518 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 14.36 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1926 helix: 1.82 (0.16), residues: 1070 sheet: -2.09 (0.36), residues: 158 loop : -1.04 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 739 TYR 0.033 0.002 TYR A 707 PHE 0.016 0.002 PHE D 515 TRP 0.008 0.001 TRP A 762 HIS 0.007 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00582 (15354) covalent geometry : angle 0.62292 (20772) SS BOND : bond 0.00312 ( 8) SS BOND : angle 1.11657 ( 16) hydrogen bonds : bond 0.03999 ( 878) hydrogen bonds : angle 4.34671 ( 2550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.577 Fit side-chains REVERT: A 469 ASP cc_start: 0.6287 (m-30) cc_final: 0.5096 (m-30) REVERT: B 442 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7181 (mp) REVERT: C 469 ASP cc_start: 0.6352 (m-30) cc_final: 0.5116 (m-30) REVERT: I 227 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7731 (mp) outliers start: 41 outliers final: 31 residues processed: 277 average time/residue: 0.1149 time to fit residues: 48.9710 Evaluate side-chains 280 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 442 LEU 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 89 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 185 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.204630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177895 restraints weight = 18191.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.171922 restraints weight = 25499.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169428 restraints weight = 25933.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170195 restraints weight = 26585.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170504 restraints weight = 21781.607| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15362 Z= 0.125 Angle : 0.529 9.411 20788 Z= 0.271 Chirality : 0.041 0.193 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.459 59.388 2518 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1926 helix: 2.11 (0.16), residues: 1072 sheet: -1.80 (0.40), residues: 132 loop : -0.94 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 48 TYR 0.041 0.001 TYR A 707 PHE 0.012 0.001 PHE D 495 TRP 0.012 0.001 TRP C 762 HIS 0.011 0.002 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00291 (15354) covalent geometry : angle 0.52869 (20772) SS BOND : bond 0.00238 ( 8) SS BOND : angle 0.90650 ( 16) hydrogen bonds : bond 0.03376 ( 878) hydrogen bonds : angle 4.11393 ( 2550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.589 Fit side-chains REVERT: A 469 ASP cc_start: 0.5926 (m-30) cc_final: 0.4730 (m-30) REVERT: C 469 ASP cc_start: 0.6001 (m-30) cc_final: 0.4770 (m-30) REVERT: C 707 TYR cc_start: 0.7584 (t80) cc_final: 0.7230 (t80) REVERT: I 227 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7666 (mp) outliers start: 38 outliers final: 24 residues processed: 278 average time/residue: 0.1186 time to fit residues: 50.3930 Evaluate side-chains 278 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 597 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 183 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 = 0.4227 r_free = 0.4227 target = 0.198662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164796 restraints weight = 18460.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152448 restraints weight = 24813.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150961 restraints weight = 29115.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150893 restraints weight = 25835.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150669 restraints weight = 23121.019| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15362 Z= 0.208 Angle : 0.590 8.792 20788 Z= 0.300 Chirality : 0.044 0.217 2394 Planarity : 0.004 0.044 2544 Dihedral : 10.735 59.744 2518 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 15.47 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1926 helix: 1.93 (0.16), residues: 1070 sheet: -1.89 (0.37), residues: 158 loop : -0.98 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 711 TYR 0.025 0.002 TYR A 707 PHE 0.014 0.002 PHE D 515 TRP 0.007 0.001 TRP B 605 HIS 0.007 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00505 (15354) covalent geometry : angle 0.58888 (20772) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.19769 ( 16) hydrogen bonds : bond 0.03782 ( 878) hydrogen bonds : angle 4.25689 ( 2550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 259 time to evaluate : 0.590 Fit side-chains REVERT: A 469 ASP cc_start: 0.6361 (m-30) cc_final: 0.5089 (m-30) REVERT: A 711 ARG cc_start: 0.3735 (mmp-170) cc_final: 0.3376 (mmp-170) REVERT: C 469 ASP cc_start: 0.6332 (m-30) cc_final: 0.4975 (m-30) REVERT: I 48 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.6503 (ttm-80) REVERT: I 227 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7739 (mp) REVERT: J 198 HIS cc_start: 0.7317 (t-90) cc_final: 0.7094 (t-170) outliers start: 41 outliers final: 33 residues processed: 277 average time/residue: 0.1198 time to fit residues: 50.2615 Evaluate side-chains 283 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 643 THR 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 742 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 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 ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.204164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173634 restraints weight = 18348.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.164291 restraints weight = 24983.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.161503 restraints weight = 27280.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162294 restraints weight = 25574.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162521 restraints weight = 19687.406| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15362 Z= 0.132 Angle : 0.539 10.114 20788 Z= 0.274 Chirality : 0.041 0.164 2394 Planarity : 0.004 0.043 2544 Dihedral : 10.132 59.631 2518 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.28 % Allowed : 16.23 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1926 helix: 2.07 (0.16), residues: 1076 sheet: -1.96 (0.38), residues: 164 loop : -0.85 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 48 TYR 0.039 0.001 TYR A 707 PHE 0.014 0.001 PHE B 491 TRP 0.009 0.001 TRP J 203 HIS 0.008 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00310 (15354) covalent geometry : angle 0.53871 (20772) SS BOND : bond 0.00143 ( 8) SS BOND : angle 1.00367 ( 16) hydrogen bonds : bond 0.03340 ( 878) hydrogen bonds : angle 4.12337 ( 2550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.510 Fit side-chains REVERT: A 469 ASP cc_start: 0.6220 (m-30) cc_final: 0.5591 (m-30) REVERT: C 469 ASP cc_start: 0.6190 (m-30) cc_final: 0.4840 (m-30) REVERT: D 486 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6107 (mm-30) REVERT: I 42 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7214 (p0) REVERT: I 227 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7775 (mp) REVERT: J 42 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7218 (p0) outliers start: 33 outliers final: 26 residues processed: 272 average time/residue: 0.1155 time to fit residues: 47.8086 Evaluate side-chains 282 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 643 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 442 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 42 ASP Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 134 optimal weight: 0.0070 chunk 74 optimal weight: 1.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- 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 ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.204893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174944 restraints weight = 18320.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166314 restraints weight = 24933.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.163539 restraints weight = 26872.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163589 restraints weight = 24228.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163191 restraints weight = 21434.788| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15362 Z= 0.124 Angle : 0.533 10.023 20788 Z= 0.270 Chirality : 0.041 0.166 2394 Planarity : 0.004 0.043 2544 Dihedral : 9.649 59.075 2518 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.14 % Allowed : 16.37 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 1926 helix: 2.13 (0.16), residues: 1074 sheet: -1.74 (0.39), residues: 158 loop : -0.78 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 48 TYR 0.035 0.001 TYR C 707 PHE 0.017 0.001 PHE B 491 TRP 0.008 0.001 TRP D 605 HIS 0.007 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00290 (15354) covalent geometry : angle 0.53271 (20772) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.92270 ( 16) hydrogen bonds : bond 0.03268 ( 878) hydrogen bonds : angle 4.10102 ( 2550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 269 time to evaluate : 0.682 Fit side-chains REVERT: A 469 ASP cc_start: 0.6180 (m-30) cc_final: 0.4864 (m-30) REVERT: A 813 LYS cc_start: 0.6036 (mtpp) cc_final: 0.5063 (tttt) REVERT: C 469 ASP cc_start: 0.6207 (m-30) cc_final: 0.4855 (m-30) REVERT: D 486 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5562 (mm-30) REVERT: I 42 ASP cc_start: 0.7468 (p0) cc_final: 0.7234 (p0) REVERT: I 48 ARG cc_start: 0.7039 (ttm-80) cc_final: 0.6802 (ttm110) REVERT: I 198 HIS cc_start: 0.7168 (t-90) cc_final: 0.6956 (t-170) REVERT: I 227 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7789 (mp) REVERT: J 42 ASP cc_start: 0.7424 (p0) cc_final: 0.7188 (p0) REVERT: J 48 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6712 (ttm110) outliers start: 31 outliers final: 27 residues processed: 286 average time/residue: 0.1205 time to fit residues: 52.4394 Evaluate side-chains 289 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 597 SER Chi-restraints excluded: chain B residue 643 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 442 LEU Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 643 THR Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 227 ILE Chi-restraints excluded: chain J residue 89 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.197522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165733 restraints weight = 18451.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156127 restraints weight = 26638.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153243 restraints weight = 28026.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153480 restraints weight = 27578.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153490 restraints weight = 21602.082| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15362 Z= 0.188 Angle : 0.592 9.848 20788 Z= 0.301 Chirality : 0.043 0.180 2394 Planarity : 0.004 0.043 2544 Dihedral : 9.901 57.478 2518 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.35 % Allowed : 16.85 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1926 helix: 1.97 (0.16), residues: 1072 sheet: -1.69 (0.37), residues: 164 loop : -0.89 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 48 TYR 0.044 0.002 TYR A 707 PHE 0.026 0.002 PHE D 491 TRP 0.008 0.001 TRP D 605 HIS 0.007 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00459 (15354) covalent geometry : angle 0.59147 (20772) SS BOND : bond 0.00147 ( 8) SS BOND : angle 1.12549 ( 16) hydrogen bonds : bond 0.03664 ( 878) hydrogen bonds : angle 4.28027 ( 2550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2590.33 seconds wall clock time: 45 minutes 52.71 seconds (2752.71 seconds total)