Starting phenix.real_space_refine on Fri Jun 5 03:30:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.map" model { file = "/net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zks_74383/06_2026/9zks_74383.cif" } resolution = 3.36 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= 0.017 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 P 3 5.49 5 S 104 5.16 5 C 11221 2.51 5 N 2659 2.21 5 O 2996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16983 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2910 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 11, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 150 Chain: "B" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2950 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 12, 'ARG:plan': 6, 'PHE:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3063 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 14, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2902 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6, 'PHE:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 138 Chain: "E" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 969 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1177 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1163 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1156 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "M" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 283 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 123 Unusual residues: {'OLC': 2, 'PLM': 2, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'OLC': 2, 'PLM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 108 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.05, per 1000 atoms: 0.30 Number of scatterers: 16983 At special positions: 0 Unit cell: (130.35, 109.725, 140.25, 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) S 104 16.00 P 3 15.00 O 2996 8.00 N 2659 7.00 C 11221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 G 90 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 923.7 milliseconds 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 16 sheets defined 61.1% alpha, 5.6% 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 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 removed outlier: 3.513A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 removed outlier: 4.016A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 4.422A pdb=" N PHE A 655 " --> pdb=" O THR A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.885A pdb=" N MET A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 738 through 752 removed outlier: 3.689A pdb=" N VAL A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 744 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.969A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.596A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.787A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) 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 626 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.698A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 774 through 779 removed outlier: 3.654A pdb=" N GLY B 777 " --> pdb=" O GLY B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.564A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 removed outlier: 3.597A pdb=" N PHE C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 removed outlier: 4.063A pdb=" N TYR C 417 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 691 removed outlier: 3.511A pdb=" N ILE C 687 " --> pdb=" O GLU C 683 " (cutoff:3.500A) 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 removed outlier: 3.541A pdb=" N TRP C 763 " --> pdb=" O LYS C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 822 removed outlier: 3.893A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.082A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR D 421 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.637A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 3.593A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 486 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.704A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for '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 626 removed outlier: 3.607A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.533A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.654A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 removed outlier: 4.143A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.797A pdb=" N GLU D 755 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 774 through 779 removed outlier: 4.150A pdb=" N ASP D 779 " --> pdb=" O GLY D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 819 removed outlier: 4.072A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 Processing helix chain 'E' and resid 57 through 85 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 107 removed outlier: 3.635A pdb=" N LEU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 127 through 158 Processing helix chain 'F' and resid 4 through 40 removed outlier: 3.581A pdb=" N LYS F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 85 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 88 through 106 Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 127 through 159 removed outlier: 3.560A pdb=" N SER F 159 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 41 removed outlier: 3.587A pdb=" N THR G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 128 through 148 removed outlier: 3.606A pdb=" N ILE G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER G 148 " --> pdb=" O CYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 185 removed outlier: 3.676A pdb=" N GLY G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.982A pdb=" N TYR G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 41 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 128 through 150 removed outlier: 3.748A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG H 149 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 185 removed outlier: 3.525A pdb=" N GLY H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.586A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 298 Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.917A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 441 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 395 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 494 Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 679 removed outlier: 6.968A pdb=" N VAL A 679 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 645 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 646 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N GLU A 701 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 397 through 398 removed outlier: 3.639A pdb=" N THR B 398 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 502 through 505 removed outlier: 3.647A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 649 through 650 removed outlier: 6.656A pdb=" N THR B 649 " --> pdb=" O VAL B 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 471 through 476 removed outlier: 7.699A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 471 through 476 removed outlier: 7.699A pdb=" N ALA C 473 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA C 731 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 475 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 644 through 645 removed outlier: 7.446A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 10.238A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 700 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 397 through 398 removed outlier: 5.536A pdb=" N THR D 398 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA D 477 " --> pdb=" O GLY D 733 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLY D 733 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.758A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 82 through 84 Processing sheet with id=AB6, first strand: chain 'H' and resid 45 through 46 Processing sheet with id=AB7, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.753A pdb=" N HIS H 83 " --> pdb=" O CYS H 90 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3102 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2827 1.33 - 1.45: 4702 1.45 - 1.58: 9646 1.58 - 1.70: 6 1.70 - 1.82: 156 Bond restraints: 17337 Sorted by residual: bond pdb=" O12 POV G 501 " pdb=" P POV G 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" O12 POV D1003 " pdb=" P POV D1003 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.18e+00 bond pdb=" O12 POV A1003 " pdb=" P POV A1003 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C11 POV G 501 " pdb=" O12 POV G 501 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C11 POV D1003 " pdb=" O12 POV D1003 " ideal model delta sigma weight residual 1.408 1.456 -0.048 2.00e-02 2.50e+03 5.81e+00 ... (remaining 17332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 23238 3.59 - 7.17: 229 7.17 - 10.76: 31 10.76 - 14.34: 6 14.34 - 17.93: 1 Bond angle restraints: 23505 Sorted by residual: angle pdb=" C ALA F 125 " pdb=" N ASP F 126 " pdb=" CA ASP F 126 " ideal model delta sigma weight residual 121.54 131.81 -10.27 1.91e+00 2.74e-01 2.89e+01 angle pdb=" CA LEU H 139 " pdb=" CB LEU H 139 " pdb=" CG LEU H 139 " ideal model delta sigma weight residual 116.30 134.23 -17.93 3.50e+00 8.16e-02 2.62e+01 angle pdb=" CA GLU C 630 " pdb=" CB GLU C 630 " pdb=" CG GLU C 630 " ideal model delta sigma weight residual 114.10 123.59 -9.49 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CB MET G 35 " pdb=" CG MET G 35 " pdb=" SD MET G 35 " ideal model delta sigma weight residual 112.70 125.62 -12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C SER M 272 " pdb=" N PHE M 273 " pdb=" CA PHE M 273 " ideal model delta sigma weight residual 120.68 113.40 7.28 1.70e+00 3.46e-01 1.83e+01 ... (remaining 23500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 9874 34.56 - 69.13: 156 69.13 - 103.69: 13 103.69 - 138.26: 12 138.26 - 172.82: 2 Dihedral angle restraints: 10057 sinusoidal: 3543 harmonic: 6514 Sorted by residual: dihedral pdb=" CA VAL D 792 " pdb=" C VAL D 792 " pdb=" N ALA D 793 " pdb=" CA ALA D 793 " ideal model delta harmonic sigma weight residual 180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLU E 87 " pdb=" C GLU E 87 " pdb=" N TRP E 88 " pdb=" CA TRP E 88 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C3 POV G 501 " pdb=" C31 POV G 501 " pdb=" O31 POV G 501 " pdb=" C32 POV G 501 " ideal model delta sinusoidal sigma weight residual 172.61 -0.21 172.82 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 10054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2480 0.085 - 0.170: 246 0.170 - 0.256: 16 0.256 - 0.341: 1 0.341 - 0.426: 1 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CB ILE D 489 " pdb=" CA ILE D 489 " pdb=" CG1 ILE D 489 " pdb=" CG2 ILE D 489 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB ILE C 629 " pdb=" CA ILE C 629 " pdb=" CG1 ILE C 629 " pdb=" CG2 ILE C 629 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CG LEU A 749 " pdb=" CB LEU A 749 " pdb=" CD1 LEU A 749 " pdb=" CD2 LEU A 749 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2741 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 100 " -0.009 2.00e-02 2.50e+03 2.05e-02 8.38e+00 pdb=" CG TYR F 100 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 100 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR F 100 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR F 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 100 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 100 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR F 100 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 809 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" CD GLU C 809 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU C 809 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU C 809 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 740 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO C 741 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 741 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 741 " -0.033 5.00e-02 4.00e+02 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1304 2.74 - 3.28: 17600 3.28 - 3.82: 28775 3.82 - 4.36: 31828 4.36 - 4.90: 54863 Nonbonded interactions: 134370 Sorted by model distance: nonbonded pdb=" OE1 GLU E 87 " pdb=" OG1 THR E 90 " model vdw 2.202 3.040 nonbonded pdb=" O LYS A 665 " pdb=" OG1 THR A 668 " model vdw 2.226 3.040 nonbonded pdb=" O TYR A 764 " pdb=" OG SER A 771 " model vdw 2.249 3.040 nonbonded pdb=" O LEU F 16 " pdb=" OG SER F 19 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU C 520 " pdb=" OH TYR H 199 " model vdw 2.256 3.040 ... (remaining 134365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 through 398 or resid 400 through 402 o \ r (resid 403 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 422 or resid 424 th \ rough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 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 461 or (res \ id 462 and (name N or name CA or name C or name O or name CB )) or resid 463 thr \ ough 466 or (resid 468 through 469 and (name N or name CA or name C or name O or \ name CB )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and \ (name N or name CA or name C or name O or name CB )) or resid 484 through 486 or \ (resid 487 and (name N or name CA or name C or name O or name CB )) or resid 48 \ 8 through 501 or (resid 502 and (name N or name CA or name C or name O or name C \ B )) or resid 503 through 540 or (resid 541 through 542 and (name N or name CA o \ r name C or name O or name CB )) or resid 543 or (resid 565 through 566 and (nam \ e N or name CA or name C or name O or name CB )) or resid 567 through 581 or res \ id 583 through 629 or (resid 630 and (name N or name CA or name C or name O or n \ ame CB )) or resid 631 through 635 or (resid 637 through 640 and (name N or name \ CA or name C or name O or name CB )) or resid 641 through 646 or resid 649 or ( \ resid 650 and (name N or name CA or name C or name O or name CB )) or resid 651 \ through 662 or (resid 663 and (name N or name CA or name C or name O or name CB \ )) or (resid 665 through 666 and (name N or name CA or name C or name O or name \ CB )) or resid 667 through 670 or resid 672 through 675 or (resid 676 and (name \ N or name CA or name C or name O or name CB )) or resid 677 through 682 or resid \ 684 through 685 or resid 688 through 689 or (resid 690 through 693 and (name N \ or name CA or name C or name O or name CB )) or resid 694 through 733 or (resid \ 734 and (name N or name CA or name C or name O or name CB )) or resid 735 throug \ h 736 or resid 738 through 739 or resid 742 through 749 or (resid 751 and (name \ N or name CA or name C or name O or name CB )) or resid 752 through 753 or resid \ 755 through 759 or (resid 761 and (name N or name CA or name C or name O or nam \ e CB )) or resid 762 through 771 or (resid 776 through 777 and (name N or name C \ A or name C or name O or name CB )) or resid 779 through 795 or resid 797 throug \ h 811 or (resid 812 through 813 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'B' and (resid 397 through 398 or (resid 399 and (name N or name CA or na \ me C or name O or name CB )) or resid 400 through 401 or (resid 402 and (name N \ or name CA or name C or name O or name CB )) or resid 404 through 407 or resid 4 \ 09 through 411 or resid 416 through 418 or resid 420 through 426 or resid 428 th \ rough 435 or resid 437 or resid 440 or (resid 442 and (name N or name CA or name \ C or name O or name CB )) or resid 444 through 445 or resid 447 through 452 or \ (resid 453 through 454 and (name N or name CA or name C or name O or name CB )) \ or (resid 456 through 458 and (name N or name CA or name C or name O or name CB \ )) or resid 460 through 470 or resid 472 through 473 or resid 475 or resid 477 t \ hrough 486 or (resid 487 and (name N or name CA or name C or name O or name CB ) \ ) or resid 488 through 489 or (resid 490 through 491 and (name N or name CA or n \ ame C or name O or name CB )) or resid 492 through 505 or (resid 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 or (r \ esid 511 and (name N or name CA or name C or name O or name CB )) or resid 512 t \ hrough 544 or (resid 545 through 546 and (name N or name CA or name C or name O \ or name CB )) or resid 547 or (resid 569 through 570 and (name N or name CA or n \ ame C or name O or name CB )) or resid 571 through 585 or resid 587 through 639 \ or resid 641 through 650 or resid 653 through 659 or (resid 660 through 661 and \ (name N or name CA or name C or name O or name CB )) or resid 662 through 667 or \ (resid 669 through 670 and (name N or name CA or name C or name O or name CB )) \ or resid 671 through 674 or resid 676 through 684 or (resid 685 and (name N or \ name CA or name C or name O or name CB )) or resid 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 and (na \ me N or name CA or name C or name O or name CB )) or resid 693 through 695 or (r \ esid 696 through 697 and (name N or name CA or name C or name O or name CB )) or \ resid 698 through 740 or resid 742 through 743 or resid 746 through 753 or (res \ id 755 and (name N or name CA or name C or name O or name CB )) or resid 756 thr \ ough 757 or resid 759 through 763 or (resid 765 and (name N or name CA or name C \ or name O or name CB )) or resid 766 through 768 or (resid 769 and (name N or n \ ame CA or name C or name O or name CB )) or resid 770 through 775 or (resid 780 \ through 781 and (name N or name CA or name C or name O or name CB )) or (resid 7 \ 83 through 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 799 or resid 801 through 817)) selection = (chain 'C' and (resid 393 through 394 or (resid 395 and (name N or name CA or na \ me C or name O or name CB )) or resid 396 through 398 or resid 400 through 402 o \ r (resid 403 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 422 or resid 424 th \ rough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 or resid 433 or resid 436 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 441 or resid 443 through 450 \ or resid 452 through 454 or resid 456 through 458 or (resid 459 and (name N or \ name CA or name C or name O or name CB )) or resid 460 through 461 or (resid 462 \ and (name N or name CA or name C or name O or name CB )) or resid 463 through 4 \ 66 or (resid 468 through 469 and (name N or name CA or name C or name O or name \ CB )) or resid 471 or resid 473 through 481 or (resid 482 through 483 and (name \ N or name CA or name C or name O or name CB )) or resid 484 through 485 or (resi \ d 486 through 487 and (name N or name CA or name C or name O or name CB )) or re \ sid 488 through 501 or (resid 502 and (name N or name CA or name C or name O or \ name CB )) or resid 503 through 540 or (resid 541 through 542 and (name N or nam \ e CA or name C or name O or name CB )) or resid 543 or (resid 565 through 566 an \ d (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 629 or (resid 630 and (name N or name CA or name C or name \ O or name CB )) or resid 631 through 635 or (resid 637 through 640 and (name N o \ r name CA or name C or name O or name CB )) or resid 641 through 646 or resid 64 \ 9 or (resid 650 and (name N or name CA or name C or name O or name CB )) or resi \ d 651 or (resid 652 through 653 and (name N or name CA or name C or name O or na \ me CB )) or resid 654 through 662 or (resid 663 and (name N or name CA or name C \ or name O or name CB )) or (resid 665 through 666 and (name N or name CA or nam \ e C or name O or name CB )) or resid 667 through 669 or (resid 670 and (name N o \ r name CA or name C or name O or name CB )) or resid 672 through 675 or (resid 6 \ 76 and (name N or name CA or name C or name O or name CB )) or resid 677 through \ 682 or resid 684 through 685 or (resid 688 and (name N or name CA or name C or \ name O or name CB )) or resid 689 or (resid 690 through 693 and (name N or name \ CA or name C or name O or name CB )) or resid 694 through 733 or (resid 734 and \ (name N or name CA or name C or name O or name CB )) or resid 735 through 736 or \ resid 738 through 739 or resid 742 through 749 or (resid 751 and (name N or nam \ e CA or name C or name O or name CB )) or resid 752 through 753 or resid 755 thr \ ough 759 or resid 761 through 771 or (resid 776 through 777 and (name N or name \ CA or name C or name O or name CB )) or resid 779 through 795 or resid 797 throu \ gh 811 or (resid 812 through 813 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'D' and (resid 397 through 401 or (resid 402 and (name N or name CA or na \ me C or name O or name CB )) or resid 404 through 407 or resid 409 through 411 o \ r resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or res \ id 437 or resid 440 or (resid 442 and (name N or name CA or name C or name O or \ name CB )) or resid 444 through 445 or resid 447 through 452 or (resid 453 throu \ gh 454 and (name N or name CA or name C or name O or name CB )) or (resid 456 th \ rough 458 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 462 or (resid 463 and (name N or name CA or name C or name O or name CB \ )) or resid 464 through 470 or resid 472 through 473 or resid 475 or resid 477 t \ hrough 486 or (resid 487 and (name N or name CA or name C or name O or name CB ) \ ) or resid 488 through 489 or (resid 490 through 491 and (name N or name CA or n \ ame C or name O or name CB )) or resid 492 through 507 or (resid 508 through 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 or (resid \ 511 and (name N or name CA or name C or name O or name CB )) or resid 512 throu \ gh 585 or resid 587 through 639 or resid 641 through 650 or resid 653 through 66 \ 6 or (resid 667 and (name N or name CA or name C or name O or name CB )) or (res \ id 669 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 674 or resid 676 through 684 or (resid 685 and (name N or name \ CA or name C or name O or name CB )) or resid 686 or (resid 688 and (name N or n \ ame CA or name C or name O or name CB )) or resid 689 or (resid 692 and (name N \ or name CA or name C or name O or name CB )) or resid 693 or (resid 694 through \ 697 and (name N or name CA or name C or name O or name CB )) or resid 698 throug \ h 714 or (resid 715 through 716 and (name N or name CA or name C or name O or na \ me CB )) or resid 717 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 through 743 or re \ sid 746 through 753 or resid 755 through 757 or resid 759 through 763 or (resid \ 765 and (name N or name CA or name C or name O or name CB )) or resid 766 throug \ h 768 or (resid 769 and (name N or name CA or name C or name O or name CB )) or \ resid 770 through 775 or resid 780 through 781 or (resid 783 through 784 and (na \ me N or name CA or name C or name O or name CB )) or resid 785 through 799 or re \ sid 801 through 817)) } ncs_group { reference = (chain 'G' and (resid 19 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 231)) selection = chain 'H' } 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 individual isotropic 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: 4.800 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.680 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.005 0.063 17343 Z= 0.231 Angle : 0.924 17.927 23517 Z= 0.455 Chirality : 0.051 0.426 2744 Planarity : 0.005 0.059 2863 Dihedral : 14.685 172.824 5875 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.32 (0.16), residues: 2221 helix: -0.09 (0.13), residues: 1327 sheet: -2.32 (0.47), residues: 120 loop : -1.89 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 590 TYR 0.048 0.002 TYR F 100 PHE 0.039 0.002 PHE E 23 TRP 0.021 0.002 TRP D 766 HIS 0.013 0.002 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (17337) covalent geometry : angle 0.92420 / 0.46 (23505) SS BOND : bond 0.00216 / 0.11 ( 6) SS BOND : angle 1.02515 / 0.59 ( 12) hydrogen bonds : bond 0.13170 / 9.17 ( 1055) hydrogen bonds : angle 5.77468 / 4.08 ( 3102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.653 Fit side-chains REVERT: A 465 TYR cc_start: 0.7204 (m-80) cc_final: 0.6772 (m-80) REVERT: A 590 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8187 (mmt180) REVERT: A 663 PHE cc_start: 0.8971 (m-10) cc_final: 0.8767 (m-10) REVERT: A 717 MET cc_start: 0.7638 (tmm) cc_final: 0.7396 (tmm) REVERT: A 759 LYS cc_start: 0.9142 (tptm) cc_final: 0.8925 (tptm) REVERT: B 469 TYR cc_start: 0.7883 (m-80) cc_final: 0.7673 (m-80) REVERT: B 587 GLN cc_start: 0.8443 (mp-120) cc_final: 0.7869 (mp10) REVERT: B 705 GLU cc_start: 0.8162 (mp0) cc_final: 0.7696 (pm20) REVERT: B 747 ASN cc_start: 0.8429 (m110) cc_final: 0.7975 (m110) REVERT: B 764 ASN cc_start: 0.8942 (m110) cc_final: 0.8514 (m110) REVERT: C 391 TYR cc_start: 0.8493 (m-80) cc_final: 0.8207 (m-80) REVERT: C 438 LEU cc_start: 0.8271 (mm) cc_final: 0.8023 (mp) REVERT: C 475 LEU cc_start: 0.8859 (tp) cc_final: 0.8497 (tp) REVERT: C 524 CYS cc_start: 0.8408 (m) cc_final: 0.8074 (m) REVERT: C 640 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7440 (tt0) REVERT: C 738 LEU cc_start: 0.8695 (mp) cc_final: 0.8240 (tt) REVERT: C 743 ASN cc_start: 0.9131 (m-40) cc_final: 0.8768 (m-40) REVERT: C 809 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 685 THR cc_start: 0.8688 (p) cc_final: 0.8112 (p) REVERT: D 688 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7453 (pt0) REVERT: D 713 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8035 (tt0) REVERT: D 714 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7922 (mm-40) REVERT: D 765 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7993 (ttmm) REVERT: D 782 GLU cc_start: 0.5528 (mp0) cc_final: 0.4140 (tt0) REVERT: E 148 TYR cc_start: 0.8723 (t80) cc_final: 0.8346 (t80) REVERT: F 55 LYS cc_start: 0.7690 (tmtt) cc_final: 0.7136 (mmmt) REVERT: G 106 PHE cc_start: 0.4541 (t80) cc_final: 0.4321 (t80) REVERT: H 198 HIS cc_start: 0.7110 (t-90) cc_final: 0.6865 (m90) outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.1234 time to fit residues: 82.1642 Evaluate side-chains 323 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN M 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.154997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111651 restraints weight = 36366.674| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.27 r_work: 0.3397 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 17343 Z= 0.314 Angle : 0.724 10.031 23517 Z= 0.379 Chirality : 0.045 0.168 2744 Planarity : 0.004 0.056 2863 Dihedral : 11.280 136.187 2733 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.70 % Allowed : 12.56 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -0.33 (0.18), residues: 2221 helix: 0.88 (0.14), residues: 1318 sheet: -2.07 (0.44), residues: 135 loop : -1.80 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 586 TYR 0.026 0.002 TYR G 201 PHE 0.037 0.002 PHE M 273 TRP 0.016 0.002 TRP A 456 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.31 (17337) covalent geometry : angle 0.72305 / 0.38 (23505) SS BOND : bond 0.00393 / 0.22 ( 6) SS BOND : angle 1.63195 / 0.95 ( 12) hydrogen bonds : bond 0.04959 / 3.34 ( 1055) hydrogen bonds : angle 4.64393 / 3.29 ( 3102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 MET cc_start: 0.7916 (tmm) cc_final: 0.7660 (tmm) REVERT: A 794 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 708 MET cc_start: 0.8412 (tmm) cc_final: 0.8026 (tmm) REVERT: B 747 ASN cc_start: 0.8583 (m110) cc_final: 0.8163 (m110) REVERT: C 640 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7312 (tt0) REVERT: C 738 LEU cc_start: 0.8622 (mp) cc_final: 0.8195 (tt) REVERT: D 408 MET cc_start: 0.8310 (tpp) cc_final: 0.7887 (tpp) REVERT: D 713 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8367 (tt0) REVERT: D 714 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8215 (mm-40) REVERT: D 758 LEU cc_start: 0.8616 (mm) cc_final: 0.8283 (tp) REVERT: D 765 LYS cc_start: 0.8729 (tmmt) cc_final: 0.8167 (ttmm) REVERT: F 55 LYS cc_start: 0.7774 (tmtt) cc_final: 0.7311 (mmtm) REVERT: F 94 ASN cc_start: 0.8501 (m-40) cc_final: 0.7951 (m110) REVERT: G 44 TRP cc_start: 0.8437 (m100) cc_final: 0.7958 (m-10) REVERT: G 106 PHE cc_start: 0.4884 (t80) cc_final: 0.4454 (t80) REVERT: H 35 MET cc_start: 0.8597 (mmm) cc_final: 0.8381 (mmm) REVERT: H 41 THR cc_start: 0.8309 (t) cc_final: 0.8068 (p) outliers start: 43 outliers final: 28 residues processed: 341 average time/residue: 0.1231 time to fit residues: 65.8384 Evaluate side-chains 328 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 825 CYS Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 283 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 16 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 747 ASN C 583 GLN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.158225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112757 restraints weight = 36519.542| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.10 r_work: 0.3473 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17343 Z= 0.146 Angle : 0.581 9.865 23517 Z= 0.298 Chirality : 0.040 0.196 2744 Planarity : 0.003 0.043 2863 Dihedral : 10.317 125.919 2733 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.08 % Allowed : 13.94 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.24 (0.18), residues: 2221 helix: 1.40 (0.14), residues: 1328 sheet: -2.19 (0.47), residues: 128 loop : -1.65 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 53 TYR 0.021 0.001 TYR D 523 PHE 0.023 0.001 PHE D 541 TRP 0.014 0.001 TRP A 456 HIS 0.004 0.001 HIS E 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (17337) covalent geometry : angle 0.58030 / 0.30 (23505) SS BOND : bond 0.00253 / 0.14 ( 6) SS BOND : angle 1.13353 / 0.65 ( 12) hydrogen bonds : bond 0.04231 / 2.85 ( 1055) hydrogen bonds : angle 4.22193 / 2.99 ( 3102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.8327 (tpp) cc_final: 0.7904 (tpt) REVERT: A 499 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8814 (ptm) REVERT: A 717 MET cc_start: 0.7796 (tmm) cc_final: 0.7545 (tmm) REVERT: A 794 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8526 (mp) REVERT: B 709 ASN cc_start: 0.9336 (t0) cc_final: 0.9129 (t0) REVERT: B 710 GLU cc_start: 0.7823 (pp20) cc_final: 0.7334 (pp20) REVERT: B 714 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: C 701 GLU cc_start: 0.8303 (pm20) cc_final: 0.7834 (pm20) REVERT: C 738 LEU cc_start: 0.8547 (mp) cc_final: 0.8199 (tt) REVERT: D 408 MET cc_start: 0.8329 (tpp) cc_final: 0.7920 (tpp) REVERT: D 511 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: D 685 THR cc_start: 0.8715 (p) cc_final: 0.8408 (p) REVERT: D 688 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7293 (pt0) REVERT: D 714 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8243 (mm-40) REVERT: D 758 LEU cc_start: 0.8681 (mm) cc_final: 0.8326 (tp) REVERT: D 765 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8259 (ttmm) REVERT: E 11 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8279 (mpp) REVERT: E 148 TYR cc_start: 0.8364 (t80) cc_final: 0.8136 (t80) REVERT: F 55 LYS cc_start: 0.7666 (tmtt) cc_final: 0.7228 (mmtm) REVERT: G 43 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.7176 (m-10) REVERT: G 44 TRP cc_start: 0.8281 (m100) cc_final: 0.8048 (m-10) REVERT: G 106 PHE cc_start: 0.4919 (t80) cc_final: 0.4499 (t80) REVERT: H 41 THR cc_start: 0.8262 (t) cc_final: 0.8039 (p) outliers start: 49 outliers final: 27 residues processed: 351 average time/residue: 0.1214 time to fit residues: 67.9911 Evaluate side-chains 351 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 405 TYR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 157 optimal weight: 0.4980 chunk 101 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS C 638 GLN ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS H 172 ASN M 298 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.157585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112580 restraints weight = 36289.651| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.03 r_work: 0.3479 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17343 Z= 0.142 Angle : 0.584 15.013 23517 Z= 0.295 Chirality : 0.041 0.222 2744 Planarity : 0.003 0.045 2863 Dihedral : 9.724 114.677 2733 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.45 % Allowed : 16.77 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.47 (0.18), residues: 2221 helix: 1.57 (0.14), residues: 1338 sheet: -2.10 (0.48), residues: 116 loop : -1.58 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 53 TYR 0.016 0.001 TYR D 523 PHE 0.035 0.001 PHE M 273 TRP 0.021 0.001 TRP C 456 HIS 0.010 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (17337) covalent geometry : angle 0.58302 / 0.29 (23505) SS BOND : bond 0.00251 / 0.13 ( 6) SS BOND : angle 1.53930 / 0.82 ( 12) hydrogen bonds : bond 0.04029 / 2.69 ( 1055) hydrogen bonds : angle 4.10550 / 2.90 ( 3102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 MET cc_start: 0.8424 (tpp) cc_final: 0.7876 (tpp) REVERT: A 499 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8799 (ptm) REVERT: A 592 LEU cc_start: 0.8079 (tt) cc_final: 0.7766 (tt) REVERT: A 794 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8585 (mp) REVERT: C 701 GLU cc_start: 0.8271 (pm20) cc_final: 0.7912 (pm20) REVERT: C 738 LEU cc_start: 0.8570 (mp) cc_final: 0.8182 (tt) REVERT: D 408 MET cc_start: 0.8315 (tpp) cc_final: 0.7914 (tpp) REVERT: D 511 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8320 (tppt) REVERT: D 688 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7309 (pt0) REVERT: D 758 LEU cc_start: 0.8723 (mm) cc_final: 0.8429 (tp) REVERT: D 765 LYS cc_start: 0.8536 (tmmt) cc_final: 0.8329 (ttmm) REVERT: D 766 TRP cc_start: 0.8558 (t-100) cc_final: 0.8348 (t-100) REVERT: E 11 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8323 (mpp) REVERT: E 148 TYR cc_start: 0.8320 (t80) cc_final: 0.8072 (t80) REVERT: F 55 LYS cc_start: 0.7646 (tmtt) cc_final: 0.7213 (mmtm) REVERT: G 44 TRP cc_start: 0.8240 (m100) cc_final: 0.7999 (m-10) REVERT: G 106 PHE cc_start: 0.4902 (t80) cc_final: 0.4484 (t80) outliers start: 55 outliers final: 30 residues processed: 353 average time/residue: 0.1250 time to fit residues: 69.3186 Evaluate side-chains 349 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS H 172 ASN ** M 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.157400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112879 restraints weight = 36311.368| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.32 r_work: 0.3460 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17343 Z= 0.144 Angle : 0.580 13.011 23517 Z= 0.293 Chirality : 0.041 0.234 2744 Planarity : 0.003 0.045 2863 Dihedral : 9.380 112.395 2733 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.83 % Allowed : 17.96 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.61 (0.18), residues: 2221 helix: 1.70 (0.14), residues: 1332 sheet: -2.09 (0.48), residues: 116 loop : -1.54 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.016 0.001 TYR H 199 PHE 0.026 0.001 PHE D 541 TRP 0.014 0.001 TRP A 456 HIS 0.007 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17337) covalent geometry : angle 0.57988 / 0.29 (23505) SS BOND : bond 0.00260 / 0.14 ( 6) SS BOND : angle 1.23434 / 0.69 ( 12) hydrogen bonds : bond 0.03998 / 2.68 ( 1055) hydrogen bonds : angle 4.09368 / 2.88 ( 3102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: A 492 MET cc_start: 0.8426 (tpp) cc_final: 0.7854 (tpp) REVERT: A 499 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8828 (ptm) REVERT: A 592 LEU cc_start: 0.8209 (tt) cc_final: 0.7773 (tt) REVERT: A 672 SER cc_start: 0.8983 (t) cc_final: 0.8761 (p) REVERT: A 794 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8586 (mp) REVERT: B 527 MET cc_start: 0.8492 (mmm) cc_final: 0.8148 (mmt) REVERT: B 639 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7786 (tt) REVERT: B 714 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: C 701 GLU cc_start: 0.8221 (pm20) cc_final: 0.7921 (pm20) REVERT: C 738 LEU cc_start: 0.8598 (mp) cc_final: 0.8179 (tt) REVERT: D 408 MET cc_start: 0.8360 (tpp) cc_final: 0.7962 (tpp) REVERT: D 511 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8323 (tppt) REVERT: D 688 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7497 (pt0) REVERT: D 758 LEU cc_start: 0.8702 (mm) cc_final: 0.8424 (tp) REVERT: D 765 LYS cc_start: 0.8564 (tmmt) cc_final: 0.8259 (ttmm) REVERT: E 11 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8336 (mpp) REVERT: E 148 TYR cc_start: 0.8338 (t80) cc_final: 0.8095 (t80) REVERT: F 55 LYS cc_start: 0.7643 (tmtt) cc_final: 0.7211 (mmtm) REVERT: G 44 TRP cc_start: 0.8261 (m100) cc_final: 0.8041 (m-10) REVERT: G 82 THR cc_start: 0.8086 (p) cc_final: 0.7656 (t) REVERT: G 106 PHE cc_start: 0.4933 (t80) cc_final: 0.4503 (t80) REVERT: G 171 SER cc_start: 0.8745 (p) cc_final: 0.8464 (p) REVERT: M 278 VAL cc_start: 0.9104 (t) cc_final: 0.8879 (m) outliers start: 61 outliers final: 35 residues processed: 359 average time/residue: 0.1265 time to fit residues: 72.2525 Evaluate side-chains 349 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 307 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 186 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** M 298 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.155995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113519 restraints weight = 36376.493| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.43 r_work: 0.3392 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17343 Z= 0.128 Angle : 0.593 15.440 23517 Z= 0.295 Chirality : 0.041 0.298 2744 Planarity : 0.003 0.042 2863 Dihedral : 9.122 109.713 2733 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.52 % Allowed : 19.91 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.73 (0.18), residues: 2221 helix: 1.80 (0.14), residues: 1333 sheet: -1.94 (0.48), residues: 119 loop : -1.51 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.023 0.001 TYR D 523 PHE 0.028 0.001 PHE F 99 TRP 0.010 0.001 TRP A 456 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17337) covalent geometry : angle 0.59214 / 0.29 (23505) SS BOND : bond 0.00157 / 0.08 ( 6) SS BOND : angle 1.31413 / 0.72 ( 12) hydrogen bonds : bond 0.03872 / 2.59 ( 1055) hydrogen bonds : angle 4.02200 / 2.83 ( 3102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 324 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: A 492 MET cc_start: 0.8409 (tpp) cc_final: 0.7837 (tpp) REVERT: A 499 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8815 (ptm) REVERT: B 714 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: C 499 MET cc_start: 0.8814 (tmm) cc_final: 0.7560 (tmm) REVERT: C 701 GLU cc_start: 0.8244 (pm20) cc_final: 0.7939 (pm20) REVERT: C 704 MET cc_start: 0.8929 (tpp) cc_final: 0.8516 (tpp) REVERT: C 724 ASP cc_start: 0.8721 (p0) cc_final: 0.8298 (p0) REVERT: C 738 LEU cc_start: 0.8597 (mp) cc_final: 0.8164 (tt) REVERT: D 408 MET cc_start: 0.8378 (tpp) cc_final: 0.7995 (tpp) REVERT: D 511 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8384 (tppt) REVERT: D 758 LEU cc_start: 0.8688 (mm) cc_final: 0.8345 (tp) REVERT: D 765 LYS cc_start: 0.8534 (tmmt) cc_final: 0.8212 (ttmm) REVERT: E 11 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (mpp) REVERT: E 148 TYR cc_start: 0.8417 (t80) cc_final: 0.8116 (t80) REVERT: F 55 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7147 (mmtm) REVERT: G 82 THR cc_start: 0.7852 (p) cc_final: 0.7442 (t) REVERT: G 106 PHE cc_start: 0.5020 (t80) cc_final: 0.4520 (t80) REVERT: G 171 SER cc_start: 0.8820 (p) cc_final: 0.8570 (p) REVERT: M 278 VAL cc_start: 0.9097 (t) cc_final: 0.8853 (m) outliers start: 56 outliers final: 33 residues processed: 351 average time/residue: 0.1229 time to fit residues: 68.6461 Evaluate side-chains 348 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 310 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 574 PHE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 286 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 5 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 HIS ** M 298 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.151824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109636 restraints weight = 35746.773| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.25 r_work: 0.3326 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 17343 Z= 0.302 Angle : 0.723 15.361 23517 Z= 0.369 Chirality : 0.045 0.261 2744 Planarity : 0.004 0.045 2863 Dihedral : 10.232 124.339 2733 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.58 % Allowed : 21.11 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.24 (0.18), residues: 2221 helix: 1.41 (0.14), residues: 1335 sheet: -2.17 (0.46), residues: 125 loop : -1.70 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 53 TYR 0.027 0.002 TYR G 226 PHE 0.032 0.002 PHE D 541 TRP 0.034 0.002 TRP G 44 HIS 0.005 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.30 (17337) covalent geometry : angle 0.72231 / 0.37 (23505) SS BOND : bond 0.00422 / 0.22 ( 6) SS BOND : angle 1.60237 / 0.89 ( 12) hydrogen bonds : bond 0.04756 / 3.19 ( 1055) hydrogen bonds : angle 4.47532 / 3.17 ( 3102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: A 492 MET cc_start: 0.8687 (tpp) cc_final: 0.8203 (tpt) REVERT: A 499 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8755 (ptm) REVERT: A 592 LEU cc_start: 0.8436 (tt) cc_final: 0.8228 (tt) REVERT: A 801 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9048 (tt) REVERT: B 700 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.6031 (t80) REVERT: B 714 GLN cc_start: 0.8732 (mp10) cc_final: 0.7834 (mp10) REVERT: B 747 ASN cc_start: 0.8749 (m-40) cc_final: 0.8470 (m-40) REVERT: C 701 GLU cc_start: 0.8392 (pm20) cc_final: 0.8152 (pm20) REVERT: C 704 MET cc_start: 0.8937 (tpp) cc_final: 0.8436 (tpp) REVERT: C 738 LEU cc_start: 0.8620 (mp) cc_final: 0.8168 (tt) REVERT: D 408 MET cc_start: 0.8450 (tpp) cc_final: 0.8170 (tpp) REVERT: D 511 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8385 (tppt) REVERT: D 688 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7697 (pt0) REVERT: E 11 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8228 (mpp) REVERT: E 94 ASN cc_start: 0.7657 (m-40) cc_final: 0.7389 (m110) REVERT: E 148 TYR cc_start: 0.8436 (t80) cc_final: 0.8169 (t80) REVERT: F 55 LYS cc_start: 0.7678 (tmtt) cc_final: 0.7203 (mmtm) REVERT: F 94 ASN cc_start: 0.8733 (m-40) cc_final: 0.8520 (m-40) REVERT: G 106 PHE cc_start: 0.5327 (t80) cc_final: 0.4599 (t80) REVERT: G 171 SER cc_start: 0.8790 (p) cc_final: 0.8538 (p) REVERT: M 278 VAL cc_start: 0.9243 (t) cc_final: 0.8952 (m) outliers start: 57 outliers final: 36 residues processed: 338 average time/residue: 0.1229 time to fit residues: 65.9708 Evaluate side-chains 339 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Chi-restraints excluded: chain M residue 286 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 76 optimal weight: 0.0370 chunk 164 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 130 optimal weight: 0.0980 chunk 120 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN M 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.114636 restraints weight = 35791.038| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.10 r_work: 0.3428 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17343 Z= 0.135 Angle : 0.630 18.327 23517 Z= 0.312 Chirality : 0.041 0.291 2744 Planarity : 0.003 0.042 2863 Dihedral : 9.557 117.740 2733 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.14 % Allowed : 22.80 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.60 (0.18), residues: 2221 helix: 1.70 (0.14), residues: 1334 sheet: -2.13 (0.49), residues: 110 loop : -1.58 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 53 TYR 0.019 0.001 TYR G 226 PHE 0.029 0.001 PHE D 541 TRP 0.020 0.001 TRP G 44 HIS 0.004 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (17337) covalent geometry : angle 0.62975 / 0.31 (23505) SS BOND : bond 0.00220 / 0.12 ( 6) SS BOND : angle 1.27502 / 0.71 ( 12) hydrogen bonds : bond 0.04053 / 2.72 ( 1055) hydrogen bonds : angle 4.17857 / 2.96 ( 3102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 487 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6971 (m-80) REVERT: A 492 MET cc_start: 0.8501 (tpp) cc_final: 0.7978 (tpt) REVERT: A 499 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8707 (ptm) REVERT: A 592 LEU cc_start: 0.8083 (tt) cc_final: 0.7826 (tt) REVERT: A 752 GLN cc_start: 0.8275 (pt0) cc_final: 0.7350 (tm-30) REVERT: A 801 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9114 (mt) REVERT: B 527 MET cc_start: 0.8497 (mmm) cc_final: 0.8125 (mmt) REVERT: C 701 GLU cc_start: 0.8235 (pm20) cc_final: 0.7998 (pm20) REVERT: C 704 MET cc_start: 0.8900 (tpp) cc_final: 0.8466 (tpp) REVERT: C 724 ASP cc_start: 0.8675 (p0) cc_final: 0.8299 (p0) REVERT: C 738 LEU cc_start: 0.8574 (mp) cc_final: 0.8151 (tt) REVERT: D 408 MET cc_start: 0.8404 (tpp) cc_final: 0.8050 (tpp) REVERT: D 511 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8415 (tppt) REVERT: D 671 TRP cc_start: 0.7730 (t60) cc_final: 0.7243 (m100) REVERT: D 688 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7645 (pt0) REVERT: D 756 GLN cc_start: 0.8167 (pt0) cc_final: 0.7807 (mm110) REVERT: D 758 LEU cc_start: 0.8513 (mm) cc_final: 0.8144 (tp) REVERT: E 11 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8299 (mpp) REVERT: E 148 TYR cc_start: 0.8395 (t80) cc_final: 0.8128 (t80) REVERT: F 55 LYS cc_start: 0.7572 (tmtt) cc_final: 0.7122 (mmtm) REVERT: G 82 THR cc_start: 0.7973 (p) cc_final: 0.7555 (t) REVERT: G 106 PHE cc_start: 0.5116 (t80) cc_final: 0.4437 (t80) REVERT: G 171 SER cc_start: 0.8757 (p) cc_final: 0.8520 (p) REVERT: M 278 VAL cc_start: 0.9047 (t) cc_final: 0.8835 (m) outliers start: 50 outliers final: 32 residues processed: 349 average time/residue: 0.1182 time to fit residues: 65.7066 Evaluate side-chains 341 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 811 CYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 283 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 220 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 62 optimal weight: 7.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.157927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115384 restraints weight = 36101.034| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.46 r_work: 0.3427 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17343 Z= 0.130 Angle : 0.642 15.514 23517 Z= 0.315 Chirality : 0.042 0.343 2744 Planarity : 0.003 0.042 2863 Dihedral : 9.119 113.317 2733 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.51 % Allowed : 23.99 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.73 (0.18), residues: 2221 helix: 1.81 (0.14), residues: 1333 sheet: -2.01 (0.47), residues: 119 loop : -1.52 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 53 TYR 0.018 0.001 TYR D 523 PHE 0.042 0.001 PHE F 146 TRP 0.020 0.001 TRP G 44 HIS 0.006 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (17337) covalent geometry : angle 0.64099 / 0.32 (23505) SS BOND : bond 0.00312 / 0.19 ( 6) SS BOND : angle 1.32859 / 0.72 ( 12) hydrogen bonds : bond 0.03997 / 2.69 ( 1055) hydrogen bonds : angle 4.12621 / 2.92 ( 3102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 325 time to evaluate : 0.697 Fit side-chains REVERT: A 487 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: A 492 MET cc_start: 0.8493 (tpp) cc_final: 0.8119 (tpp) REVERT: A 499 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8752 (ptm) REVERT: A 592 LEU cc_start: 0.8063 (tt) cc_final: 0.7809 (tt) REVERT: A 749 LEU cc_start: 0.9043 (mt) cc_final: 0.8796 (mm) REVERT: A 801 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9122 (mt) REVERT: B 527 MET cc_start: 0.8605 (mmm) cc_final: 0.8219 (mmt) REVERT: B 714 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: B 747 ASN cc_start: 0.8698 (m-40) cc_final: 0.8371 (m110) REVERT: C 701 GLU cc_start: 0.8275 (pm20) cc_final: 0.7980 (pm20) REVERT: C 704 MET cc_start: 0.8949 (tpp) cc_final: 0.8511 (tpp) REVERT: C 724 ASP cc_start: 0.8651 (p0) cc_final: 0.8284 (p0) REVERT: C 738 LEU cc_start: 0.8594 (mp) cc_final: 0.8169 (tt) REVERT: D 408 MET cc_start: 0.8385 (tpp) cc_final: 0.8036 (tpp) REVERT: D 511 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8347 (tppt) REVERT: D 671 TRP cc_start: 0.7747 (t60) cc_final: 0.7408 (m100) REVERT: D 688 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7508 (pt0) REVERT: D 765 LYS cc_start: 0.8501 (tmmt) cc_final: 0.8277 (ttmm) REVERT: E 11 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8374 (mpp) REVERT: E 148 TYR cc_start: 0.8405 (t80) cc_final: 0.8146 (t80) REVERT: F 55 LYS cc_start: 0.7550 (tmtt) cc_final: 0.7095 (mmtm) REVERT: F 123 MET cc_start: 0.4554 (pmm) cc_final: 0.4213 (pmm) REVERT: G 82 THR cc_start: 0.7794 (p) cc_final: 0.7384 (t) REVERT: G 106 PHE cc_start: 0.5143 (t80) cc_final: 0.4257 (t80) REVERT: G 171 SER cc_start: 0.8804 (p) cc_final: 0.8570 (p) REVERT: M 278 VAL cc_start: 0.8973 (t) cc_final: 0.8742 (m) outliers start: 40 outliers final: 29 residues processed: 345 average time/residue: 0.1197 time to fit residues: 65.5198 Evaluate side-chains 345 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 286 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 4 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 209 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 HIS ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 298 GLN ** 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 = 0.4248 r_free = 0.4248 target = 0.158227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115358 restraints weight = 36314.648| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.46 r_work: 0.3430 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17343 Z= 0.133 Angle : 0.666 15.340 23517 Z= 0.324 Chirality : 0.042 0.351 2744 Planarity : 0.003 0.041 2863 Dihedral : 8.921 110.557 2733 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.51 % Allowed : 23.74 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.75 (0.18), residues: 2221 helix: 1.83 (0.14), residues: 1326 sheet: -2.01 (0.47), residues: 119 loop : -1.50 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 53 TYR 0.028 0.001 TYR F 72 PHE 0.035 0.001 PHE F 146 TRP 0.035 0.001 TRP G 44 HIS 0.004 0.001 HIS F 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17337) covalent geometry : angle 0.66523 / 0.32 (23505) SS BOND : bond 0.00226 / 0.13 ( 6) SS BOND : angle 1.40954 / 0.76 ( 12) hydrogen bonds : bond 0.03961 / 2.67 ( 1055) hydrogen bonds : angle 4.11984 / 2.92 ( 3102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4442 Ramachandran restraints generated. 2221 Oldfield, 0 Emsley, 2221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.697 Fit side-chains REVERT: A 487 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: A 492 MET cc_start: 0.8498 (tpp) cc_final: 0.8098 (tpp) REVERT: A 499 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8784 (ptm) REVERT: A 592 LEU cc_start: 0.8030 (tt) cc_final: 0.7766 (tt) REVERT: A 801 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9136 (mt) REVERT: B 527 MET cc_start: 0.8609 (mmm) cc_final: 0.8307 (mmt) REVERT: B 714 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: B 747 ASN cc_start: 0.8706 (m-40) cc_final: 0.8371 (m110) REVERT: C 701 GLU cc_start: 0.8247 (pm20) cc_final: 0.7930 (pm20) REVERT: C 704 MET cc_start: 0.8937 (tpp) cc_final: 0.8500 (tpp) REVERT: C 724 ASP cc_start: 0.8643 (p0) cc_final: 0.8273 (p0) REVERT: C 738 LEU cc_start: 0.8594 (mp) cc_final: 0.8172 (tt) REVERT: D 408 MET cc_start: 0.8380 (tpp) cc_final: 0.8049 (tpp) REVERT: D 511 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8315 (tppt) REVERT: D 671 TRP cc_start: 0.7748 (t60) cc_final: 0.7440 (m100) REVERT: D 688 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7552 (pt0) REVERT: D 765 LYS cc_start: 0.8499 (tmmt) cc_final: 0.8264 (ttmm) REVERT: E 11 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8344 (mpp) REVERT: E 148 TYR cc_start: 0.8398 (t80) cc_final: 0.8134 (t80) REVERT: F 55 LYS cc_start: 0.7556 (tmtt) cc_final: 0.7097 (mmtm) REVERT: F 123 MET cc_start: 0.4689 (pmm) cc_final: 0.4343 (pmm) REVERT: F 148 TYR cc_start: 0.8623 (t80) cc_final: 0.8305 (t80) REVERT: G 82 THR cc_start: 0.7722 (p) cc_final: 0.7309 (t) REVERT: M 278 VAL cc_start: 0.8965 (t) cc_final: 0.8723 (m) outliers start: 40 outliers final: 30 residues processed: 339 average time/residue: 0.1177 time to fit residues: 63.7156 Evaluate side-chains 345 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 499 MET Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 619 PHE Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 700 TYR Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 17 CYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 286 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 151 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 298 GLN ** 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 = 0.4240 r_free = 0.4240 target = 0.157492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.114416 restraints weight = 36366.891| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.54 r_work: 0.3411 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17343 Z= 0.149 Angle : 0.676 15.160 23517 Z= 0.330 Chirality : 0.043 0.360 2744 Planarity : 0.003 0.043 2863 Dihedral : 8.828 111.014 2733 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.39 % Allowed : 23.87 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.72 (0.18), residues: 2221 helix: 1.81 (0.14), residues: 1325 sheet: -2.01 (0.47), residues: 119 loop : -1.52 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 53 TYR 0.040 0.001 TYR G 179 PHE 0.032 0.001 PHE F 146 TRP 0.028 0.001 TRP G 44 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17337) covalent geometry : angle 0.67503 / 0.33 (23505) SS BOND : bond 0.00274 / 0.16 ( 6) SS BOND : angle 1.40980 / 0.76 ( 12) hydrogen bonds : bond 0.04056 / 2.73 ( 1055) hydrogen bonds : angle 4.14377 / 2.93 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5112.69 seconds wall clock time: 88 minutes 9.42 seconds (5289.42 seconds total)