Starting phenix.real_space_refine on Fri Jun 5 00:53:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkw_74387/06_2026/9zkw_74387.map" } resolution = 3.33 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= 0.019 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 5 5.49 5 S 97 5.16 5 C 10642 2.51 5 N 2547 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s 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: 16169 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2976 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "B" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2983 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'PHE:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2976 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 11, 'PHE:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "E" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1428 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1174 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1172 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 164} Chain breaks: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 7, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" 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: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 101 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 138 Unusual residues: {'OLC': 2, 'PLM': 1, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'OLC': 2, 'PLM': 2, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.28, per 1000 atoms: 0.26 Number of scatterers: 16169 At special positions: 0 Unit cell: (114.675, 119.625, 134.475, 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 97 16.00 P 5 15.00 O 2878 8.00 N 2547 7.00 C 10642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, 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 E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.04 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.02 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " 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: 1.66 Conformation dependent library (CDL) restraints added in 798.0 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 22 sheets defined 57.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.697A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.570A pdb=" N GLU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.904A pdb=" N LYS A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 711 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.724A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 3.679A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.655A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 643 removed outlier: 4.020A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 696 through 698 No H-bonds generated for 'chain 'B' and resid 696 through 698' Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 793 through 819 removed outlier: 3.808A pdb=" N VAL B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.807A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 431 Processing helix chain 'C' and resid 451 through 454 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 540 Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.730A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.649A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 681 through 691 Processing helix chain 'C' and resid 702 through 711 removed outlier: 3.572A pdb=" N TYR C 707 " --> pdb=" O THR C 703 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.514A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.695A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 4.296A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 694 Processing helix chain 'D' and resid 706 through 712 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.587A pdb=" N ASN D 747 " --> pdb=" O ARG D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 777 through 781 removed outlier: 3.588A pdb=" N SER D 780 " --> pdb=" O GLY D 777 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS D 781 " --> pdb=" O GLY D 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 777 through 781' Processing helix chain 'D' and resid 793 through 819 Processing helix chain 'E' and resid 5 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.651A pdb=" N ILE E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.872A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.927A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 40 Processing helix chain 'G' and resid 118 through 128 Processing helix chain 'G' and resid 128 through 150 removed outlier: 3.820A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 184 removed outlier: 4.342A pdb=" N LEU G 159 " --> pdb=" O ARG G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 231 removed outlier: 3.656A 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 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 128 through 147 removed outlier: 3.572A pdb=" N ILE H 132 " --> pdb=" O SER H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 150 No H-bonds generated for 'chain 'H' and resid 148 through 150' Processing helix chain 'H' and resid 157 through 184 Processing helix chain 'H' and resid 202 through 231 removed outlier: 3.930A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 395 Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 449 removed outlier: 3.661A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.820A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.147A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.147A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 476 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA B 477 " --> pdb=" O GLY B 733 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.502A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.557A pdb=" N ASP B 454 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.636A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 392 through 395 Processing sheet with id=AB3, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB4, first strand: chain 'C' and resid 448 through 450 Processing sheet with id=AB5, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB6, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.555A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.867A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.656A pdb=" N ASP D 490 " --> pdb=" O THR D 736 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.822A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 682 through 683 removed outlier: 8.195A pdb=" N VAL D 683 " --> pdb=" O TYR D 647 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR D 649 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 701 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 650 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N GLU D 705 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 34 through 39 Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 102 removed outlier: 4.023A pdb=" N VAL G 101 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 89 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 101 through 102 970 hydrogen bonds defined for protein. 2814 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: 3.09 Time building geometry restraints manager: 1.96 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: 2822 1.33 - 1.45: 4607 1.45 - 1.58: 8898 1.58 - 1.71: 10 1.71 - 1.84: 153 Bond restraints: 16490 Sorted by residual: bond pdb=" O12 POV C1004 " pdb=" P POV C1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" O12 POV C1003 " pdb=" P POV C1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" O12 POV B1003 " pdb=" P POV B1003 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" O12 POV E 401 " pdb=" P POV E 401 " ideal model delta sigma weight residual 1.657 1.608 0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C11 POV B1003 " pdb=" O12 POV B1003 " ideal model delta sigma weight residual 1.408 1.457 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 16485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 22077 3.05 - 6.10: 186 6.10 - 9.15: 15 9.15 - 12.20: 7 12.20 - 15.25: 1 Bond angle restraints: 22286 Sorted by residual: angle pdb=" C VAL E 8 " pdb=" N GLN E 9 " pdb=" CA GLN E 9 " ideal model delta sigma weight residual 121.14 112.15 8.99 1.75e+00 3.27e-01 2.64e+01 angle pdb=" CB MET E 10 " pdb=" CG MET E 10 " pdb=" SD MET E 10 " ideal model delta sigma weight residual 112.70 127.95 -15.25 3.00e+00 1.11e-01 2.58e+01 angle pdb=" N GLU E 191 " pdb=" CA GLU E 191 " pdb=" CB GLU E 191 " ideal model delta sigma weight residual 110.12 116.52 -6.40 1.47e+00 4.63e-01 1.90e+01 angle pdb=" CA GLN E 9 " pdb=" CB GLN E 9 " pdb=" CG GLN E 9 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N GLN E 9 " pdb=" CA GLN E 9 " pdb=" CB GLN E 9 " ideal model delta sigma weight residual 110.40 116.49 -6.09 1.63e+00 3.76e-01 1.40e+01 ... (remaining 22281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 9437 34.79 - 69.58: 182 69.58 - 104.37: 12 104.37 - 139.16: 12 139.16 - 173.96: 4 Dihedral angle restraints: 9647 sinusoidal: 3565 harmonic: 6082 Sorted by residual: dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 158.43 -65.43 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS E 67 " pdb=" SG CYS E 67 " pdb=" SG CYS E 77 " pdb=" CB CYS E 77 " ideal model delta sinusoidal sigma weight residual 93.00 34.14 58.86 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual -86.00 -141.63 55.63 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 9644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2072 0.056 - 0.112: 420 0.112 - 0.168: 58 0.168 - 0.223: 4 0.223 - 0.279: 2 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CB VAL C 535 " pdb=" CA VAL C 535 " pdb=" CG1 VAL C 535 " pdb=" CG2 VAL C 535 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA GLU E 191 " pdb=" N GLU E 191 " pdb=" C GLU E 191 " pdb=" CB GLU E 191 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA GLN E 9 " pdb=" N GLN E 9 " pdb=" C GLN E 9 " pdb=" CB GLN E 9 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2553 not shown) Planarity restraints: 2719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " -0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO A 516 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 520 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 142 " -0.014 2.00e-02 2.50e+03 1.74e-02 5.28e+00 pdb=" CG PHE E 142 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 142 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 142 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE E 142 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 142 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 142 " 0.000 2.00e-02 2.50e+03 ... (remaining 2716 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4336 2.80 - 3.33: 15568 3.33 - 3.85: 26788 3.85 - 4.38: 29715 4.38 - 4.90: 52107 Nonbonded interactions: 128514 Sorted by model distance: nonbonded pdb=" OG1 THR D 649 " pdb=" OG1 THR D 655 " model vdw 2.280 3.040 nonbonded pdb=" O VAL H 21 " pdb=" OG1 THR H 24 " model vdw 2.281 3.040 nonbonded pdb=" O VAL C 677 " pdb=" OH TYR C 696 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR A 478 " pdb=" OE2 GLU D 755 " model vdw 2.287 3.040 nonbonded pdb=" O PRO A 589 " pdb=" NH1 ARG A 595 " model vdw 2.291 3.120 ... (remaining 128509 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 403 o \ r resid 405 through 407 or resid 412 through 414 or resid 416 through 422 or res \ id 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 through 4 \ 41 or resid 443 through 450 or resid 452 through 454 or resid 456 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 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 5 \ 43 or (resid 565 and (name N or name CA or name C or name O or name CB )) or res \ id 566 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 throug \ h 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 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 or (resid 652 through 653 and (name N or name CA or nam \ e C or name O or name CB )) or resid 654 through 656 or (resid 657 and (name N o \ r name CA or name C or name O or name CB )) or resid 658 through 663 or resid 66 \ 5 through 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) 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 690 or (resid 691 through 693 and (name N or name CA or name C or na \ me O or name CB )) or resid 694 through 736 or resid 738 through 739 or resid 74 \ 2 through 749 or resid 751 through 753 or resid 755 through 759 or resid 761 thr \ ough 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 through 811 or (resid 812 thro \ ugh 813 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' 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 or (resid 410 \ through 411 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 16 through 418 or (resid 420 and (name N or name CA or name C or name O or name \ CB )) or resid 421 or (resid 422 and (name N or name CA or name C or name O or n \ ame CB )) or resid 423 through 426 or resid 428 through 435 or resid 437 or resi \ d 440 or resid 442 or resid 444 through 445 or resid 447 through 452 or (resid 4 \ 53 through 454 and (name N or name CA or name C or name O or name CB )) or (resi \ d 456 through 458 and (name N or name CA or name C or name O or name CB )) or re \ sid 460 through 470 or resid 472 through 473 or resid 475 or resid 477 through 4 \ 86 or (resid 487 and (name N or name CA or name C or name O or name CB )) or res \ id 488 through 504 or (resid 505 and (name N or name CA or name C or name O or n \ ame CB )) or resid 506 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 through 585 or resid 587 \ through 639 or (resid 641 through 644 and (name N or name CA or name C or name O \ or name CB )) or resid 645 through 650 or resid 653 or (resid 654 and (name N o \ r name CA or name C or name O or name CB )) or resid 655 through 667 or resid 66 \ 9 through 674 or resid 676 through 684 or (resid 685 and (name N or name CA or n \ ame 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 through 695 or (resi \ d 696 through 697 and (name N or name CA or name C or name O or name CB )) or re \ sid 698 through 714 or (resid 715 through 716 and (name N or name CA or name C o \ r name O or name CB )) or resid 717 through 740 or resid 742 through 743 or resi \ d 746 through 753 or resid 755 through 757 or resid 759 through 763 or resid 765 \ through 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 (name N or name CA or name C or name O or name CB )) or resid 785 through 79 \ 9 or resid 801 through 815 or (resid 816 through 817 and (name N or name CA or n \ ame C or name O or name CB )))) 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 403 o \ r resid 405 through 407 or resid 412 through 414 or resid 416 through 422 or res \ id 424 through 431 or resid 433 or resid 436 or resid 438 or resid 440 through 4 \ 41 or resid 443 through 450 or resid 452 through 454 or resid 456 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 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 5 \ 43 or (resid 565 and (name N or name CA or name C or name O or name CB )) or res \ id 566 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 throug \ h 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thro \ ugh 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 or (resid 652 through 653 and (name N or name CA or nam \ e C or name O or name CB )) or resid 654 through 656 or (resid 657 and (name N o \ r name CA or name C or name O or name CB )) or resid 658 through 663 or resid 66 \ 5 through 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) 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 690 or (resid 691 through 693 and (name N or name CA or name C or na \ me O or name CB )) or resid 694 or (resid 695 and (name N or name CA or name C o \ r name O or name CB )) or resid 696 through 710 or (resid 711 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 through 739 or resid 742 through 749 or resid 751 throu \ gh 753 or resid 755 through 759 or resid 761 through 771 or (resid 776 through 7 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 779 through \ 795 or resid 797 through 811 or (resid 812 through 813 and (name N or name CA o \ r name C or name O or name 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 and (name N or name CA or name C or name O \ or name CB )) or resid 421 through 426 or resid 428 through 435 or resid 437 or \ resid 440 or resid 442 or resid 444 through 445 or resid 447 through 452 or (re \ sid 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 465 or (resid 466 and (name N or name CA or name C or name \ O or name CB )) or resid 467 through 470 or resid 472 through 473 or resid 475 o \ r resid 477 through 486 or (resid 487 and (name N or name CA or name C or name O \ or name CB )) or resid 488 through 504 or (resid 505 and (name N or name CA or \ name C or name O or name CB )) or resid 506 through 507 or (resid 508 through 50 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 510 or (resi \ d 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thro \ ugh 585 or resid 587 through 639 or resid 641 through 650 or resid 653 through 6 \ 60 or (resid 661 and (name N or name CA or name C or name O or name CB )) or res \ id 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) or \ resid 664 through 667 or resid 669 through 674 or resid 676 through 683 or (res \ id 684 through 685 and (name N or name CA or name C or name O or name CB )) or r \ esid 686 or (resid 688 and (name N or name CA or name C or name O or name CB )) \ or resid 689 or resid 692 through 694 or (resid 695 through 697 and (name N or n \ ame CA or name C or name O or name CB )) or resid 698 through 714 or (resid 715 \ through 716 and (name N or name CA or name C or name O or name CB )) or resid 71 \ 7 through 740 or resid 742 through 743 or resid 746 through 753 or resid 755 thr \ ough 757 or resid 759 through 763 or resid 765 through 768 or (resid 769 and (na \ me N or name CA or name C or name O or name CB )) or resid 770 through 775 or re \ sid 780 through 781 or (resid 783 through 784 and (name N or name CA or name C o \ r name O or name CB )) or resid 785 through 799 or resid 801 through 817)) } ncs_group { reference = (chain 'G' and (resid 19 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 231)) selection = (chain 'H' 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)) } 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: 6.320 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.140 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.004 0.053 16500 Z= 0.209 Angle : 0.734 15.251 22306 Z= 0.367 Chirality : 0.045 0.279 2556 Planarity : 0.005 0.080 2719 Dihedral : 15.173 173.956 5745 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.20 % Allowed : 0.33 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -0.45 (0.18), residues: 2092 helix: 1.00 (0.15), residues: 1187 sheet: -1.83 (0.48), residues: 106 loop : -2.12 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 599 TYR 0.022 0.001 TYR H 226 PHE 0.040 0.002 PHE E 142 TRP 0.013 0.001 TRP A 601 HIS 0.008 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (16490) covalent geometry : angle 0.73175 / 0.37 (22286) SS BOND : bond 0.00519 / 0.33 ( 10) SS BOND : angle 2.00478 / 1.20 ( 20) hydrogen bonds : bond 0.13431 / 9.13 ( 967) hydrogen bonds : angle 5.39030 / 3.88 ( 2814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 404 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ASP cc_start: 0.8410 (t70) cc_final: 0.8169 (t0) REVERT: A 486 ASP cc_start: 0.7714 (t0) cc_final: 0.6917 (t0) REVERT: A 586 ASP cc_start: 0.6949 (t0) cc_final: 0.6731 (t0) REVERT: A 749 LEU cc_start: 0.8667 (mm) cc_final: 0.8364 (mm) REVERT: B 435 HIS cc_start: 0.8316 (t-90) cc_final: 0.8065 (t-90) REVERT: B 509 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8555 (ptmt) REVERT: B 519 ASP cc_start: 0.8417 (m-30) cc_final: 0.8181 (m-30) REVERT: B 591 ILE cc_start: 0.7920 (pt) cc_final: 0.7604 (pt) REVERT: B 629 MET cc_start: 0.7665 (ttt) cc_final: 0.7319 (ttp) REVERT: B 761 LYS cc_start: 0.8705 (ptmm) cc_final: 0.8425 (tptt) REVERT: C 403 MET cc_start: 0.6140 (mtt) cc_final: 0.5805 (mtp) REVERT: C 421 CYS cc_start: 0.7880 (m) cc_final: 0.7431 (m) REVERT: C 475 LEU cc_start: 0.7129 (tp) cc_final: 0.6923 (tp) REVERT: C 652 LYS cc_start: 0.7616 (tttm) cc_final: 0.7125 (mtpp) REVERT: C 667 TRP cc_start: 0.7255 (t-100) cc_final: 0.6949 (t-100) REVERT: C 707 TYR cc_start: 0.8174 (t80) cc_final: 0.7561 (t80) REVERT: D 427 ASP cc_start: 0.8026 (p0) cc_final: 0.7646 (p0) REVERT: D 527 MET cc_start: 0.7747 (ttm) cc_final: 0.7419 (ttm) REVERT: D 647 TYR cc_start: 0.7085 (p90) cc_final: 0.6826 (p90) REVERT: E 10 MET cc_start: 0.8595 (mpp) cc_final: 0.8347 (mmp) REVERT: E 95 GLU cc_start: 0.7797 (pp20) cc_final: 0.7369 (tp30) REVERT: E 132 HIS cc_start: 0.6260 (m-70) cc_final: 0.6039 (m170) REVERT: E 141 PHE cc_start: 0.8450 (m-10) cc_final: 0.7937 (m-80) REVERT: E 160 ASN cc_start: 0.8560 (m110) cc_final: 0.8178 (m110) REVERT: E 189 ILE cc_start: 0.9104 (tp) cc_final: 0.8562 (tp) REVERT: E 192 MET cc_start: 0.8461 (mpp) cc_final: 0.7566 (mpp) REVERT: E 196 LEU cc_start: 0.9469 (mm) cc_final: 0.9051 (mp) REVERT: E 200 MET cc_start: 0.9402 (ttm) cc_final: 0.8705 (mtp) REVERT: E 203 ASP cc_start: 0.8844 (m-30) cc_final: 0.8241 (m-30) REVERT: G 32 PHE cc_start: 0.8569 (t80) cc_final: 0.8283 (t80) REVERT: G 199 TYR cc_start: 0.7863 (p90) cc_final: 0.7611 (p90) REVERT: H 156 ASN cc_start: 0.7904 (m-40) cc_final: 0.7446 (m110) REVERT: H 203 TRP cc_start: 0.7059 (p-90) cc_final: 0.6855 (p-90) outliers start: 3 outliers final: 1 residues processed: 406 average time/residue: 0.1182 time to fit residues: 72.0432 Evaluate side-chains 303 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN D 619 ASN ** E 9 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 = 0.4082 r_free = 0.4082 target = 0.165023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.133406 restraints weight = 26776.580| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.63 r_work: 0.3443 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16500 Z= 0.115 Angle : 0.523 6.865 22306 Z= 0.273 Chirality : 0.040 0.155 2556 Planarity : 0.004 0.067 2719 Dihedral : 11.320 162.760 2645 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.56 % Allowed : 8.86 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.55 (0.19), residues: 2092 helix: 1.91 (0.15), residues: 1184 sheet: -2.42 (0.51), residues: 99 loop : -1.70 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 590 TYR 0.024 0.001 TYR E 174 PHE 0.025 0.001 PHE D 546 TRP 0.010 0.001 TRP G 44 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16490) covalent geometry : angle 0.52261 / 0.27 (22286) SS BOND : bond 0.00901 / 0.67 ( 10) SS BOND : angle 1.10513 / 0.64 ( 20) hydrogen bonds : bond 0.03611 / 2.40 ( 967) hydrogen bonds : angle 4.07350 / 2.98 ( 2814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 315 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7134 (mmp-170) cc_final: 0.6926 (mmp-170) REVERT: A 586 ASP cc_start: 0.6813 (t0) cc_final: 0.6560 (t0) REVERT: A 662 VAL cc_start: 0.8774 (m) cc_final: 0.8530 (m) REVERT: A 749 LEU cc_start: 0.8714 (mm) cc_final: 0.8401 (mt) REVERT: B 508 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 421 CYS cc_start: 0.7386 (m) cc_final: 0.7135 (m) REVERT: C 541 ARG cc_start: 0.7640 (mmp-170) cc_final: 0.7356 (mmp-170) REVERT: C 652 LYS cc_start: 0.8367 (tttm) cc_final: 0.7937 (mtpp) REVERT: C 704 MET cc_start: 0.8422 (mmm) cc_final: 0.8167 (mmt) REVERT: C 707 TYR cc_start: 0.8648 (t80) cc_final: 0.8202 (t80) REVERT: C 784 SER cc_start: 0.8549 (t) cc_final: 0.8303 (m) REVERT: D 408 MET cc_start: 0.8789 (mmm) cc_final: 0.8537 (mmt) REVERT: E 131 ARG cc_start: 0.6549 (ptp-170) cc_final: 0.6037 (mmm160) REVERT: E 141 PHE cc_start: 0.8582 (m-10) cc_final: 0.7954 (m-80) REVERT: E 160 ASN cc_start: 0.8510 (m110) cc_final: 0.7933 (m110) REVERT: E 189 ILE cc_start: 0.8928 (tp) cc_final: 0.8288 (tp) REVERT: E 192 MET cc_start: 0.8263 (mpp) cc_final: 0.7699 (mpp) REVERT: E 196 LEU cc_start: 0.9361 (mm) cc_final: 0.9107 (mm) REVERT: E 200 MET cc_start: 0.9129 (ttm) cc_final: 0.8766 (mtm) REVERT: H 87 TRP cc_start: 0.6519 (m-10) cc_final: 0.5847 (m100) REVERT: H 156 ASN cc_start: 0.7967 (m-40) cc_final: 0.7320 (m110) outliers start: 24 outliers final: 13 residues processed: 330 average time/residue: 0.1184 time to fit residues: 58.6480 Evaluate side-chains 285 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 83 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 171 optimal weight: 0.0050 chunk 157 optimal weight: 0.2980 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN D 619 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.163178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126952 restraints weight = 26691.792| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.54 r_work: 0.3442 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16500 Z= 0.121 Angle : 0.503 8.407 22306 Z= 0.264 Chirality : 0.039 0.171 2556 Planarity : 0.004 0.056 2719 Dihedral : 10.336 123.807 2643 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.76 % Allowed : 12.96 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.81 (0.19), residues: 2092 helix: 2.12 (0.15), residues: 1196 sheet: -2.46 (0.55), residues: 87 loop : -1.65 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 692 TYR 0.024 0.001 TYR G 179 PHE 0.029 0.001 PHE C 542 TRP 0.007 0.001 TRP B 766 HIS 0.004 0.001 HIS H 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16490) covalent geometry : angle 0.50287 / 0.26 (22286) SS BOND : bond 0.00650 / 0.45 ( 10) SS BOND : angle 0.98139 / 0.59 ( 20) hydrogen bonds : bond 0.03442 / 2.29 ( 967) hydrogen bonds : angle 3.84928 / 2.85 ( 2814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 508 GLN cc_start: 0.8359 (tm-30) cc_final: 0.8062 (pm20) REVERT: C 421 CYS cc_start: 0.7412 (m) cc_final: 0.7195 (m) REVERT: C 541 ARG cc_start: 0.7554 (mmp-170) cc_final: 0.7258 (mmp-170) REVERT: C 704 MET cc_start: 0.8332 (mmm) cc_final: 0.8087 (mmt) REVERT: C 707 TYR cc_start: 0.8657 (t80) cc_final: 0.8230 (t80) REVERT: D 408 MET cc_start: 0.8775 (mmm) cc_final: 0.8435 (mmt) REVERT: E 30 THR cc_start: 0.8094 (t) cc_final: 0.7884 (m) REVERT: E 99 ARG cc_start: 0.8487 (mtm110) cc_final: 0.8058 (mtm110) REVERT: E 141 PHE cc_start: 0.8618 (m-10) cc_final: 0.8112 (m-80) REVERT: E 160 ASN cc_start: 0.8319 (m-40) cc_final: 0.7881 (m-40) REVERT: E 200 MET cc_start: 0.8857 (ttm) cc_final: 0.8612 (mtp) REVERT: H 156 ASN cc_start: 0.7896 (m-40) cc_final: 0.7307 (m110) outliers start: 27 outliers final: 18 residues processed: 323 average time/residue: 0.1107 time to fit residues: 54.5824 Evaluate side-chains 289 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 141 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN C 710 GLN D 619 ASN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.160760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129503 restraints weight = 26789.139| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.69 r_work: 0.3367 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16500 Z= 0.118 Angle : 0.510 8.617 22306 Z= 0.267 Chirality : 0.040 0.170 2556 Planarity : 0.004 0.063 2719 Dihedral : 10.114 115.970 2643 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.76 % Allowed : 15.90 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.94 (0.19), residues: 2092 helix: 2.25 (0.15), residues: 1194 sheet: -2.17 (0.52), residues: 102 loop : -1.63 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 628 TYR 0.022 0.001 TYR G 179 PHE 0.031 0.001 PHE C 542 TRP 0.007 0.001 TRP B 766 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (16490) covalent geometry : angle 0.50832 / 0.27 (22286) SS BOND : bond 0.00795 / 0.56 ( 10) SS BOND : angle 1.37492 / 0.86 ( 20) hydrogen bonds : bond 0.03332 / 2.21 ( 967) hydrogen bonds : angle 3.75929 / 2.78 ( 2814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 508 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8230 (tm-30) REVERT: C 667 TRP cc_start: 0.7575 (t-100) cc_final: 0.7344 (t-100) REVERT: C 707 TYR cc_start: 0.8707 (t80) cc_final: 0.8242 (t80) REVERT: E 131 ARG cc_start: 0.6332 (ptp-170) cc_final: 0.6094 (mmm160) REVERT: E 141 PHE cc_start: 0.8650 (m-10) cc_final: 0.8153 (m-80) REVERT: E 160 ASN cc_start: 0.8185 (m-40) cc_final: 0.7780 (m110) REVERT: E 189 ILE cc_start: 0.8920 (tp) cc_final: 0.8443 (tp) REVERT: E 192 MET cc_start: 0.8301 (mpp) cc_final: 0.7746 (mpp) REVERT: E 199 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7581 (t-90) REVERT: E 200 MET cc_start: 0.8909 (ttm) cc_final: 0.8633 (mtp) REVERT: H 156 ASN cc_start: 0.7929 (m-40) cc_final: 0.7312 (m110) outliers start: 27 outliers final: 19 residues processed: 299 average time/residue: 0.1091 time to fit residues: 50.7885 Evaluate side-chains 289 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 227 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.159507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127689 restraints weight = 26745.652| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.71 r_work: 0.3357 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16500 Z= 0.133 Angle : 0.529 10.299 22306 Z= 0.276 Chirality : 0.040 0.160 2556 Planarity : 0.004 0.071 2719 Dihedral : 10.083 107.364 2643 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.28 % Allowed : 16.42 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.95 (0.19), residues: 2092 helix: 2.26 (0.15), residues: 1196 sheet: -2.44 (0.48), residues: 116 loop : -1.56 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 628 TYR 0.024 0.001 TYR H 226 PHE 0.027 0.001 PHE C 542 TRP 0.008 0.001 TRP B 766 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (16490) covalent geometry : angle 0.52588 / 0.27 (22286) SS BOND : bond 0.00528 / 0.32 ( 10) SS BOND : angle 1.87118 / 1.16 ( 20) hydrogen bonds : bond 0.03399 / 2.26 ( 967) hydrogen bonds : angle 3.74704 / 2.78 ( 2814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 508 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8222 (pm20) REVERT: C 667 TRP cc_start: 0.7514 (t-100) cc_final: 0.7035 (t-100) REVERT: C 707 TYR cc_start: 0.8747 (t80) cc_final: 0.8453 (t80) REVERT: C 756 ASP cc_start: 0.8362 (t70) cc_final: 0.8137 (t70) REVERT: E 99 ARG cc_start: 0.8509 (mtm110) cc_final: 0.8153 (mtm110) REVERT: E 141 PHE cc_start: 0.8699 (m-10) cc_final: 0.8158 (m-80) REVERT: E 160 ASN cc_start: 0.8282 (m-40) cc_final: 0.7802 (m110) REVERT: E 192 MET cc_start: 0.8361 (mpp) cc_final: 0.7758 (mpp) REVERT: E 199 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: E 203 ASP cc_start: 0.7823 (m-30) cc_final: 0.7563 (m-30) REVERT: H 156 ASN cc_start: 0.7894 (m-40) cc_final: 0.7335 (m110) REVERT: H 228 GLU cc_start: 0.8266 (tp30) cc_final: 0.8056 (tm-30) outliers start: 35 outliers final: 28 residues processed: 305 average time/residue: 0.1055 time to fit residues: 50.9759 Evaluate side-chains 300 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 714 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** 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 = 0.4002 r_free = 0.4002 target = 0.159009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127853 restraints weight = 26901.063| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.64 r_work: 0.3347 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16500 Z= 0.138 Angle : 0.546 12.334 22306 Z= 0.281 Chirality : 0.040 0.171 2556 Planarity : 0.004 0.063 2719 Dihedral : 10.124 104.496 2643 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.41 % Allowed : 16.94 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.95 (0.19), residues: 2092 helix: 2.27 (0.15), residues: 1196 sheet: -2.47 (0.48), residues: 116 loop : -1.56 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 628 TYR 0.017 0.001 TYR E 128 PHE 0.032 0.001 PHE C 542 TRP 0.009 0.001 TRP B 766 HIS 0.005 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16490) covalent geometry : angle 0.54279 / 0.28 (22286) SS BOND : bond 0.00586 / 0.35 ( 10) SS BOND : angle 1.91344 / 1.18 ( 20) hydrogen bonds : bond 0.03419 / 2.27 ( 967) hydrogen bonds : angle 3.76270 / 2.79 ( 2814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.7336 (m) cc_final: 0.6685 (m) REVERT: C 667 TRP cc_start: 0.7529 (t-100) cc_final: 0.6984 (t-100) REVERT: C 704 MET cc_start: 0.8361 (mmm) cc_final: 0.8114 (mmt) REVERT: C 707 TYR cc_start: 0.8715 (t80) cc_final: 0.8420 (t80) REVERT: C 756 ASP cc_start: 0.8334 (t70) cc_final: 0.8130 (t70) REVERT: E 99 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8170 (mtm110) REVERT: E 128 TYR cc_start: 0.8065 (t80) cc_final: 0.7841 (t80) REVERT: E 141 PHE cc_start: 0.8745 (m-10) cc_final: 0.8204 (m-80) REVERT: E 156 TYR cc_start: 0.7770 (t80) cc_final: 0.7559 (t80) REVERT: E 160 ASN cc_start: 0.8299 (m-40) cc_final: 0.7829 (m110) REVERT: E 192 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: H 156 ASN cc_start: 0.7951 (m-40) cc_final: 0.7394 (m110) outliers start: 37 outliers final: 29 residues processed: 308 average time/residue: 0.1046 time to fit residues: 50.6593 Evaluate side-chains 300 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 92 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS B 764 ASN C 638 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.160190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128479 restraints weight = 26418.592| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.60 r_work: 0.3377 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16500 Z= 0.119 Angle : 0.545 13.097 22306 Z= 0.279 Chirality : 0.040 0.169 2556 Planarity : 0.004 0.064 2719 Dihedral : 9.915 101.352 2643 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.08 % Allowed : 18.31 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2092 helix: 2.34 (0.15), residues: 1196 sheet: -2.80 (0.49), residues: 106 loop : -1.49 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 628 TYR 0.032 0.001 TYR G 179 PHE 0.033 0.001 PHE A 542 TRP 0.026 0.001 TRP E 178 HIS 0.005 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (16490) covalent geometry : angle 0.54138 / 0.28 (22286) SS BOND : bond 0.00617 / 0.35 ( 10) SS BOND : angle 2.28722 / 1.40 ( 20) hydrogen bonds : bond 0.03322 / 2.21 ( 967) hydrogen bonds : angle 3.70854 / 2.75 ( 2814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 290 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 749 LEU cc_start: 0.8788 (mt) cc_final: 0.8512 (mp) REVERT: C 421 CYS cc_start: 0.7340 (m) cc_final: 0.6612 (m) REVERT: C 704 MET cc_start: 0.8352 (mmm) cc_final: 0.8064 (mmp) REVERT: C 707 TYR cc_start: 0.8638 (t80) cc_final: 0.8282 (t80) REVERT: C 756 ASP cc_start: 0.8346 (t70) cc_final: 0.8145 (t70) REVERT: D 408 MET cc_start: 0.8682 (mmm) cc_final: 0.8317 (mmt) REVERT: E 95 GLU cc_start: 0.7946 (tt0) cc_final: 0.7718 (tt0) REVERT: E 141 PHE cc_start: 0.8735 (m-10) cc_final: 0.8222 (m-80) REVERT: E 160 ASN cc_start: 0.8369 (m-40) cc_final: 0.7846 (m110) REVERT: E 192 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7799 (mpp) REVERT: H 156 ASN cc_start: 0.7888 (m-40) cc_final: 0.7347 (m110) outliers start: 32 outliers final: 23 residues processed: 307 average time/residue: 0.1053 time to fit residues: 50.7626 Evaluate side-chains 291 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN C 638 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118820 restraints weight = 26892.547| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.67 r_work: 0.3333 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 16500 Z= 0.164 Angle : 0.602 13.005 22306 Z= 0.307 Chirality : 0.041 0.272 2556 Planarity : 0.004 0.065 2719 Dihedral : 10.257 104.559 2643 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.54 % Allowed : 18.50 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.95 (0.19), residues: 2092 helix: 2.22 (0.15), residues: 1199 sheet: -2.49 (0.48), residues: 116 loop : -1.50 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 99 TYR 0.031 0.001 TYR G 179 PHE 0.030 0.002 PHE A 542 TRP 0.032 0.001 TRP H 203 HIS 0.004 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (16490) covalent geometry : angle 0.59311 / 0.30 (22286) SS BOND : bond 0.00619 / 0.37 ( 10) SS BOND : angle 3.53274 / 1.73 ( 20) hydrogen bonds : bond 0.03596 / 2.40 ( 967) hydrogen bonds : angle 3.83297 / 2.85 ( 2814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 749 LEU cc_start: 0.8869 (mt) cc_final: 0.8573 (mp) REVERT: C 421 CYS cc_start: 0.7544 (m) cc_final: 0.6831 (m) REVERT: C 667 TRP cc_start: 0.7433 (t-100) cc_final: 0.6870 (t-100) REVERT: C 704 MET cc_start: 0.8281 (mmm) cc_final: 0.7991 (mmp) REVERT: C 707 TYR cc_start: 0.8588 (t80) cc_final: 0.8198 (t80) REVERT: C 756 ASP cc_start: 0.8432 (t70) cc_final: 0.8231 (t70) REVERT: C 801 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8402 (tt) REVERT: E 99 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8097 (mtm110) REVERT: E 141 PHE cc_start: 0.8747 (m-10) cc_final: 0.8170 (m-80) REVERT: E 160 ASN cc_start: 0.8369 (m-40) cc_final: 0.7835 (m110) REVERT: E 192 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7741 (mpp) REVERT: G 43 TYR cc_start: 0.5870 (m-80) cc_final: 0.5656 (m-80) REVERT: H 156 ASN cc_start: 0.7957 (m-40) cc_final: 0.7406 (m-40) outliers start: 39 outliers final: 32 residues processed: 296 average time/residue: 0.1032 time to fit residues: 48.5833 Evaluate side-chains 299 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 189 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN B 508 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127237 restraints weight = 26822.752| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.83 r_work: 0.3343 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16500 Z= 0.124 Angle : 0.578 14.907 22306 Z= 0.295 Chirality : 0.040 0.171 2556 Planarity : 0.004 0.064 2719 Dihedral : 9.850 101.637 2643 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.41 % Allowed : 18.76 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.98 (0.19), residues: 2092 helix: 2.31 (0.15), residues: 1197 sheet: -2.56 (0.46), residues: 120 loop : -1.58 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 99 TYR 0.022 0.001 TYR G 179 PHE 0.029 0.001 PHE A 542 TRP 0.043 0.001 TRP E 178 HIS 0.005 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16490) covalent geometry : angle 0.57242 / 0.29 (22286) SS BOND : bond 0.00746 / 0.42 ( 10) SS BOND : angle 2.78818 / 1.52 ( 20) hydrogen bonds : bond 0.03354 / 2.23 ( 967) hydrogen bonds : angle 3.75332 / 2.79 ( 2814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 749 LEU cc_start: 0.8881 (mt) cc_final: 0.8563 (mp) REVERT: B 508 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: B 768 TYR cc_start: 0.8044 (m-80) cc_final: 0.7751 (m-80) REVERT: C 421 CYS cc_start: 0.7503 (m) cc_final: 0.6739 (m) REVERT: C 667 TRP cc_start: 0.7358 (t-100) cc_final: 0.6798 (t-100) REVERT: C 704 MET cc_start: 0.8292 (mmm) cc_final: 0.8012 (mmp) REVERT: C 707 TYR cc_start: 0.8556 (t80) cc_final: 0.8095 (t80) REVERT: C 756 ASP cc_start: 0.8433 (t70) cc_final: 0.8225 (t70) REVERT: C 801 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8375 (tt) REVERT: D 408 MET cc_start: 0.8717 (mmm) cc_final: 0.8350 (mmt) REVERT: E 99 ARG cc_start: 0.8469 (mtm110) cc_final: 0.8203 (mtm110) REVERT: E 141 PHE cc_start: 0.8737 (m-10) cc_final: 0.8179 (m-80) REVERT: E 160 ASN cc_start: 0.8215 (m-40) cc_final: 0.7694 (m110) REVERT: E 178 TRP cc_start: 0.7321 (p-90) cc_final: 0.6315 (p-90) REVERT: E 192 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7823 (mpp) REVERT: H 156 ASN cc_start: 0.7806 (m-40) cc_final: 0.7241 (m-40) outliers start: 37 outliers final: 29 residues processed: 301 average time/residue: 0.1026 time to fit residues: 49.0160 Evaluate side-chains 299 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 508 GLN Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 638 GLN D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.158670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127181 restraints weight = 26798.449| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.85 r_work: 0.3338 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16500 Z= 0.127 Angle : 0.590 14.687 22306 Z= 0.299 Chirality : 0.041 0.242 2556 Planarity : 0.004 0.064 2719 Dihedral : 9.646 101.345 2643 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.35 % Allowed : 18.50 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.97 (0.19), residues: 2092 helix: 2.28 (0.15), residues: 1199 sheet: -2.43 (0.46), residues: 120 loop : -1.58 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.024 0.001 TYR H 226 PHE 0.033 0.001 PHE A 542 TRP 0.040 0.001 TRP E 178 HIS 0.005 0.001 HIS H 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16490) covalent geometry : angle 0.58566 / 0.30 (22286) SS BOND : bond 0.00533 / 0.30 ( 10) SS BOND : angle 2.39686 / 1.38 ( 20) hydrogen bonds : bond 0.03370 / 2.24 ( 967) hydrogen bonds : angle 3.78656 / 2.83 ( 2814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 662 VAL cc_start: 0.8687 (m) cc_final: 0.8469 (m) REVERT: A 749 LEU cc_start: 0.8893 (mt) cc_final: 0.8579 (mp) REVERT: B 508 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7978 (pm20) REVERT: B 768 TYR cc_start: 0.8051 (m-80) cc_final: 0.7759 (m-80) REVERT: C 421 CYS cc_start: 0.7543 (m) cc_final: 0.6775 (m) REVERT: C 492 MET cc_start: 0.8774 (ttp) cc_final: 0.8488 (ttp) REVERT: C 707 TYR cc_start: 0.8549 (t80) cc_final: 0.8101 (t80) REVERT: C 756 ASP cc_start: 0.8423 (t70) cc_final: 0.8218 (t70) REVERT: C 801 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 408 MET cc_start: 0.8705 (mmm) cc_final: 0.8345 (mmt) REVERT: E 99 ARG cc_start: 0.8451 (mtm110) cc_final: 0.8147 (mtm110) REVERT: E 141 PHE cc_start: 0.8728 (m-10) cc_final: 0.8178 (m-80) REVERT: E 160 ASN cc_start: 0.8168 (m-40) cc_final: 0.7716 (m110) REVERT: E 178 TRP cc_start: 0.7342 (p-90) cc_final: 0.6373 (p-90) REVERT: E 192 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: H 156 ASN cc_start: 0.7827 (m-40) cc_final: 0.7299 (m-40) outliers start: 36 outliers final: 30 residues processed: 288 average time/residue: 0.1029 time to fit residues: 47.0988 Evaluate side-chains 295 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 638 GLN Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain C residue 785 LEU Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 801 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 668 ASP Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 764 ASN C 638 GLN D 435 HIS D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.156980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118985 restraints weight = 26742.100| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.65 r_work: 0.3336 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16500 Z= 0.155 Angle : 0.607 14.514 22306 Z= 0.309 Chirality : 0.042 0.230 2556 Planarity : 0.004 0.066 2719 Dihedral : 9.888 104.263 2643 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.41 % Allowed : 18.76 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: 0.90 (0.19), residues: 2092 helix: 2.18 (0.15), residues: 1201 sheet: -2.77 (0.48), residues: 106 loop : -1.51 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.018 0.001 TYR G 179 PHE 0.032 0.002 PHE A 542 TRP 0.041 0.001 TRP E 178 HIS 0.005 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (16490) covalent geometry : angle 0.60279 / 0.31 (22286) SS BOND : bond 0.00587 / 0.34 ( 10) SS BOND : angle 2.35642 / 1.39 ( 20) hydrogen bonds : bond 0.03584 / 2.39 ( 967) hydrogen bonds : angle 3.88871 / 2.90 ( 2814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.75 seconds wall clock time: 67 minutes 15.86 seconds (4035.86 seconds total)