Starting phenix.real_space_refine on Thu Mar 5 02:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oce_12805/03_2026/7oce_12805.map" } resolution = 3.1 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= 0.004 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12090 2.51 5 N 2800 2.21 5 O 3088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18092 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3013 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2975 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 2975 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 105 Chain: "J" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1284 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3013 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "E" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1248 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Unusual residues: {'E2Q': 1, 'PC1': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Unusual residues: {'E2Q': 1, 'PC1': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Unusual residues: {'E2Q': 1, 'PC1': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 96 Unusual residues: {'PC1': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 142 Unusual residues: {'E2Q': 1, 'PC1': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PC1:plan-2': 5, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Unusual residues: {'CLR': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.41, per 1000 atoms: 0.24 Number of scatterers: 18092 At special positions: 0 Unit cell: (123.05, 110.21, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 3088 8.00 N 2800 7.00 C 12090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.05 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.05 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: 1.58 Conformation dependent library (CDL) restraints added in 776.3 milliseconds 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 21 sheets defined 60.5% alpha, 8.4% 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 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.871A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.080A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 626 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.524A pdb=" N GLN A 638 " --> pdb=" O ASP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.547A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 670 Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 739 through 753 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.624A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.774A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.606A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 636 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.720A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 40 removed outlier: 3.846A pdb=" N ALA G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 40 " --> pdb=" O THR G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 67 Processing helix chain 'G' and resid 67 through 85 removed outlier: 4.228A pdb=" N GLU G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 108 Proline residue: G 96 - end of helix removed outlier: 4.054A pdb=" N ARG G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 159 Processing helix chain 'I' and resid 17 through 41 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 128 through 149 Processing helix chain 'I' and resid 157 through 184 removed outlier: 3.596A pdb=" N GLY I 162 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 184 " --> pdb=" O ILE I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 240 removed outlier: 3.543A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.774A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.607A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 822 removed outlier: 3.721A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 41 Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 128 through 149 Processing helix chain 'J' and resid 157 through 184 removed outlier: 3.597A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA J 184 " --> pdb=" O ILE J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 240 removed outlier: 3.543A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.871A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 4.080A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 626 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.523A pdb=" N GLN C 638 " --> pdb=" O ASP C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 removed outlier: 3.547A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 670 Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 739 through 753 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.623A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 40 removed outlier: 3.846A pdb=" N ALA E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 67 through 85 removed outlier: 4.228A pdb=" N GLU E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 Proline residue: E 96 - end of helix removed outlier: 4.053A pdb=" N ARG E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.497A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.610A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.408A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.643A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 100 through 102 removed outlier: 3.632A pdb=" N LEU I 45 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.609A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.844A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.406A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 100 through 102 removed outlier: 3.633A pdb=" N LEU J 45 " --> pdb=" O SER J 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 436 through 438 removed outlier: 4.868A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.497A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3363 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: 3.26 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2667 1.31 - 1.45: 5171 1.45 - 1.58: 10442 1.58 - 1.71: 8 1.71 - 1.84: 168 Bond restraints: 18456 Sorted by residual: bond pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 1.799 1.691 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C09 E2Q B2902 " pdb=" S11 E2Q B2902 " ideal model delta sigma weight residual 1.799 1.692 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C09 E2Q C2702 " pdb=" S11 E2Q C2702 " ideal model delta sigma weight residual 1.799 1.692 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 1.799 1.692 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C31 PC1 A 906 " pdb=" O31 PC1 A 906 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 18451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 23664 1.91 - 3.81: 799 3.81 - 5.72: 349 5.72 - 7.62: 6 7.62 - 9.53: 46 Bond angle restraints: 24864 Sorted by residual: angle pdb=" C32 PC1 A 906 " pdb=" C31 PC1 A 906 " pdb=" O31 PC1 A 906 " ideal model delta sigma weight residual 111.44 120.97 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C32 PC1 C2707 " pdb=" C31 PC1 C2707 " pdb=" O31 PC1 C2707 " ideal model delta sigma weight residual 111.44 120.97 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C22 PC1 D 903 " pdb=" C21 PC1 D 903 " pdb=" O21 PC1 D 903 " ideal model delta sigma weight residual 111.12 120.37 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" C22 PC1 D 909 " pdb=" C21 PC1 D 909 " pdb=" O21 PC1 D 909 " ideal model delta sigma weight residual 111.12 120.35 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" C22 PC1 B2904 " pdb=" C21 PC1 B2904 " pdb=" O21 PC1 B2904 " ideal model delta sigma weight residual 111.12 120.34 -9.22 3.00e+00 1.11e-01 9.44e+00 ... (remaining 24859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 10172 23.04 - 46.08: 654 46.08 - 69.12: 92 69.12 - 92.16: 22 92.16 - 115.20: 4 Dihedral angle restraints: 10944 sinusoidal: 4250 harmonic: 6694 Sorted by residual: dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.21 77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual -86.00 -163.19 77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual -86.00 -34.83 -51.17 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 10941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1527 0.027 - 0.053: 730 0.053 - 0.080: 351 0.080 - 0.107: 145 0.107 - 0.133: 45 Chirality restraints: 2798 Sorted by residual: chirality pdb=" CA ILE B 591 " pdb=" N ILE B 591 " pdb=" C ILE B 591 " pdb=" CB ILE B 591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE D 591 " pdb=" N ILE D 591 " pdb=" C ILE D 591 " pdb=" CB ILE D 591 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE C 396 " pdb=" N ILE C 396 " pdb=" C ILE C 396 " pdb=" CB ILE C 396 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2795 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 702 " -0.016 2.00e-02 2.50e+03 1.52e-02 4.62e+00 pdb=" CG TYR D 702 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR D 702 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR D 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 702 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 702 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 702 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 702 " 0.016 2.00e-02 2.50e+03 1.51e-02 4.57e+00 pdb=" CG TYR B 702 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 702 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 702 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 702 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 702 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 702 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 702 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 107 " 0.011 2.00e-02 2.50e+03 1.34e-02 2.68e+00 pdb=" CG HIS E 107 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS E 107 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS E 107 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS E 107 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS E 107 " 0.005 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 179 2.64 - 3.21: 16783 3.21 - 3.77: 26661 3.77 - 4.34: 37132 4.34 - 4.90: 63054 Nonbonded interactions: 143809 Sorted by model distance: nonbonded pdb=" OG1 THR D 398 " pdb=" OE2 GLU D 466 " model vdw 2.080 3.040 nonbonded pdb=" N LYS B 716 " pdb=" OE1 GLU B 772 " model vdw 2.101 3.120 nonbonded pdb=" N LYS D 716 " pdb=" OE1 GLU D 772 " model vdw 2.101 3.120 nonbonded pdb=" OG SER D 635 " pdb=" OD1 ASP D 638 " model vdw 2.121 3.040 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.121 3.040 ... (remaining 143804 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: 0.01 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 or (resid 397 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 403 or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 or resid 42 \ 4 through 431 or resid 433 or resid 436 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 441 or resid 443 through 450 \ or (resid 452 through 454 and (name N or name CA or name C or name O or name CB \ )) or resid 456 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 581 or resid 5 \ 83 through 629 or (resid 630 and (name N or name CA or name C or name O or name \ CB )) or resid 631 through 632 or (resid 633 and (name N or name CA or name C or \ name O or name CB )) or resid 634 through 635 or resid 637 or (resid 638 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 through 659 or (resid 660 through 661 and (name N or name C \ A or name C or name O or name CB )) or resid 662 through 663 or resid 665 throug \ h 670 or resid 672 through 682 or resid 684 through 685 or resid 688 through 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 through 735 or (resid 736 and (name N or name CA or name C or name O or nam \ e CB )) or resid 738 or resid 741 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 758 through \ 759 or resid 761 through 765 or (resid 766 and (name N or name CA or name C or n \ ame O or name CB )) or resid 767 through 770 or resid 772 through 795 or resid 7 \ 97 through 815 or resid 817 or resid 819 or (resid 903 through 905 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or \ name C2F or name C2G or name O21 or name O22)))) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (nam \ e N or name CA or name C or name O or name CB )) or resid 423 through 426 or res \ id 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 or (resid \ 445 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 454 or resid 456 through 458 or resid 460 or (resid 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 470 or resid 472 throug \ h 473 or resid 475 or resid 477 through 489 or (resid 490 and (name N or name CA \ or name C or name O or name CB )) or resid 491 through 507 or (resid 508 throug \ h 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thro \ ugh 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) o \ r resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 567 or resid 569 through 585 or resid 587 through 639 or resid 641 t \ hrough 650 or resid 653 through 655 or (resid 656 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 667 or resid 669 thr \ ough 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 through 674 or resid 676 through 684 or (resid 685 and (name N or n \ ame CA or name C or name O or name CB )) or resid 686 or resid 688 through 689 o \ r resid 692 through 695 or (resid 696 through 697 and (name N or name CA or name \ C or name O or name CB )) or resid 698 through 727 or (resid 728 and (name N or \ name CA or name C or name O or name CB )) or resid 729 through 740 or resid 742 \ or resid 745 through 763 or resid 765 through 774 or resid 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 819 or resid 821 or resid 823 or (resid 2904 th \ rough 2906 and (name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or \ name C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) 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 or (resid 397 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 400 through 403 or resid 4 \ 05 through 407 or resid 412 through 414 or resid 416 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 or resid 42 \ 4 through 431 or resid 433 or resid 436 or (resid 438 and (name N or name CA or \ name C or name O or name CB )) or resid 440 through 441 or resid 443 through 450 \ or (resid 452 through 454 and (name N or name CA or name C or name O or name CB \ )) or resid 456 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 581 or resid 5 \ 83 through 629 or (resid 630 and (name N or name CA or name C or name O or name \ CB )) or resid 631 through 632 or (resid 633 and (name N or name CA or name C or \ name O or name CB )) or resid 634 through 635 or resid 637 or (resid 638 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 through 659 or (resid 660 through 661 and (name N or name C \ A or name C or name O or name CB )) or resid 662 through 663 or resid 665 throug \ h 670 or resid 672 through 682 or resid 684 through 685 or resid 688 through 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 through 735 or (resid 736 and (name N or name CA or name C or name O or nam \ e CB )) or resid 738 or resid 741 through 756 or (resid 757 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or resid 758 through \ 759 or resid 761 through 765 or (resid 766 and (name N or name CA or name C or n \ ame O or name CB )) or resid 767 through 770 or resid 772 through 795 or resid 7 \ 97 through 815 or resid 817 or resid 819 or (resid 2703 through 2705 and (name C \ 21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E o \ r name C2F or name C2G or name O21 or name O22)))) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 thro \ ugh 411 or resid 416 through 418 or resid 420 through 421 or (resid 422 and (nam \ e N or name CA or name C or name O or name CB )) or resid 423 through 426 or res \ id 428 through 435 or resid 437 or resid 440 or resid 442 or resid 444 or (resid \ 445 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 454 or resid 456 through 458 or resid 460 or (resid 461 and (name N or name C \ A or name C or name O or name CB )) or resid 462 through 470 or resid 472 throug \ h 473 or resid 475 or resid 477 through 489 or (resid 490 and (name N or name CA \ or name C or name O or name CB )) or resid 491 through 507 or (resid 508 throug \ h 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thro \ ugh 546 or (resid 547 and (name N or name CA or name C or name O or name CB )) o \ r resid 548 or (resid 549 and (name N or name CA or name C or name O or name CB \ )) or resid 567 or resid 569 through 585 or resid 587 through 639 or resid 641 t \ hrough 650 or resid 653 through 655 or (resid 656 through 657 and (name N or nam \ e CA or name C or name O or name CB )) or resid 658 through 667 or resid 669 thr \ ough 671 or (resid 672 and (name N or name CA or name C or name O or name CB )) \ or resid 673 through 674 or resid 676 through 684 or (resid 685 and (name N or n \ ame CA or name C or name O or name CB )) or resid 686 or resid 688 through 689 o \ r resid 692 through 695 or (resid 696 through 697 and (name N or name CA or name \ C or name O or name CB )) or resid 698 through 727 or (resid 728 and (name N or \ name CA or name C or name O or name CB )) or resid 729 through 740 or resid 742 \ or resid 745 through 763 or resid 765 through 774 or resid 781 or (resid 783 th \ rough 784 and (name N or name CA or name C or name O or name CB )) or resid 785 \ through 799 or resid 801 through 819 or resid 821 or resid 823 or (resid 904 thr \ ough 906 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or na \ me C2D or name C2E or name C2F or name C2G or name O21 or name O22)))) } ncs_group { reference = (chain 'E' and (resid 2 through 3101 or (resid 3102 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 3103 through 3104)) selection = (chain 'G' and (resid 2 through 159 or (resid 3101 through 3102 and (name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or nam \ e C2F or name C2G or name O21 or name O22)) or resid 3103 through 3104)) } ncs_group { reference = (chain 'I' and (resid 16 through 3003 or (resid 3004 through 3005 and (name C21 \ or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name \ C28 or name C29 or name C2A or name C2B or name C2C or name C2D or name C2E or n \ ame C2F or name C2G or name O21 or name O22)))) selection = (chain 'J' and (resid 16 through 240 or (resid 2501 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name O21 or name O22)) or resid 2502 through 2505)) } 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.008 0.108 18464 Z= 0.331 Angle : 0.957 9.529 24880 Z= 0.403 Chirality : 0.041 0.133 2798 Planarity : 0.003 0.036 2992 Dihedral : 15.216 115.199 6644 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.07 (0.18), residues: 2278 helix: 1.96 (0.14), residues: 1350 sheet: -0.70 (0.43), residues: 148 loop : -1.29 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.037 0.001 TYR D 702 PHE 0.022 0.002 PHE A 542 TRP 0.012 0.001 TRP E 103 HIS 0.016 0.002 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00762 (18456) covalent geometry : angle 0.95463 (24864) SS BOND : bond 0.00962 ( 8) SS BOND : angle 2.55145 ( 16) hydrogen bonds : bond 0.11228 ( 1131) hydrogen bonds : angle 4.89455 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.675 Fit side-chains REVERT: B 817 LYS cc_start: 0.5971 (tmmt) cc_final: 0.5592 (mttt) REVERT: D 817 LYS cc_start: 0.5964 (tmmt) cc_final: 0.5583 (mttt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1249 time to fit residues: 44.9574 Evaluate side-chains 184 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN B 726 ASN ** B 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN D 714 GLN D 726 ASN D 756 GLN D 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107189 restraints weight = 20928.716| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.95 r_work: 0.2993 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18464 Z= 0.136 Angle : 0.510 9.203 24880 Z= 0.264 Chirality : 0.039 0.155 2798 Planarity : 0.004 0.040 2992 Dihedral : 11.406 59.839 3406 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.69 % Allowed : 4.82 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.81 (0.18), residues: 2278 helix: 2.53 (0.14), residues: 1384 sheet: -0.49 (0.40), residues: 166 loop : -1.09 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.019 0.001 TYR B 702 PHE 0.012 0.001 PHE B 814 TRP 0.010 0.001 TRP C 762 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00306 (18456) covalent geometry : angle 0.50979 (24864) SS BOND : bond 0.00628 ( 8) SS BOND : angle 0.52080 ( 16) hydrogen bonds : bond 0.04043 ( 1131) hydrogen bonds : angle 3.64463 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 GLU cc_start: 0.8013 (tp30) cc_final: 0.7768 (tp30) REVERT: A 485 ILE cc_start: 0.8257 (mm) cc_final: 0.7936 (tp) REVERT: A 566 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7626 (pm20) REVERT: A 704 MET cc_start: 0.8687 (tpt) cc_final: 0.8483 (tpt) REVERT: A 807 LEU cc_start: 0.8082 (tp) cc_final: 0.7824 (tp) REVERT: B 438 PHE cc_start: 0.7510 (p90) cc_final: 0.7207 (p90) REVERT: B 817 LYS cc_start: 0.6156 (tmmt) cc_final: 0.5213 (mttt) REVERT: I 158 ILE cc_start: 0.8469 (tp) cc_final: 0.8258 (mm) REVERT: D 438 PHE cc_start: 0.7513 (p90) cc_final: 0.7229 (p90) REVERT: D 817 LYS cc_start: 0.6182 (tmmt) cc_final: 0.5227 (mttt) REVERT: C 439 GLU cc_start: 0.8350 (pt0) cc_final: 0.8148 (pt0) REVERT: C 482 GLU cc_start: 0.8036 (tp30) cc_final: 0.7791 (tp30) REVERT: C 485 ILE cc_start: 0.8265 (mm) cc_final: 0.7932 (tp) REVERT: C 566 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7636 (pm20) outliers start: 11 outliers final: 6 residues processed: 221 average time/residue: 0.1271 time to fit residues: 44.0652 Evaluate side-chains 210 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 453 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 224 optimal weight: 0.0170 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN B 764 ASN G 27 HIS D 764 ASN E 27 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110740 restraints weight = 21170.260| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.03 r_work: 0.2996 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18464 Z= 0.098 Angle : 0.442 8.391 24880 Z= 0.231 Chirality : 0.038 0.159 2798 Planarity : 0.003 0.040 2992 Dihedral : 10.154 59.822 3406 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.69 % Allowed : 7.27 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.18), residues: 2278 helix: 2.93 (0.14), residues: 1384 sheet: -0.39 (0.41), residues: 166 loop : -0.89 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 65 TYR 0.020 0.001 TYR A 812 PHE 0.009 0.001 PHE A 663 TRP 0.008 0.001 TRP C 762 HIS 0.002 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00206 (18456) covalent geometry : angle 0.44173 (24864) SS BOND : bond 0.00069 ( 8) SS BOND : angle 0.47484 ( 16) hydrogen bonds : bond 0.03560 ( 1131) hydrogen bonds : angle 3.32945 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 223 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 482 GLU cc_start: 0.7977 (tp30) cc_final: 0.7712 (tp30) REVERT: A 485 ILE cc_start: 0.8286 (mm) cc_final: 0.7962 (tp) REVERT: I 48 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7972 (mtt180) REVERT: C 439 GLU cc_start: 0.8336 (pt0) cc_final: 0.8092 (pt0) REVERT: C 482 GLU cc_start: 0.7976 (tp30) cc_final: 0.7707 (tp30) REVERT: E 116 MET cc_start: 0.4172 (ttm) cc_final: 0.3957 (ttt) outliers start: 11 outliers final: 9 residues processed: 227 average time/residue: 0.1232 time to fit residues: 44.1376 Evaluate side-chains 207 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 106 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 I 20 GLN J 20 GLN C 431 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105555 restraints weight = 21204.154| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.94 r_work: 0.2972 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18464 Z= 0.127 Angle : 0.470 10.405 24880 Z= 0.243 Chirality : 0.038 0.151 2798 Planarity : 0.003 0.039 2992 Dihedral : 10.129 59.954 3406 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 8.90 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.18), residues: 2278 helix: 2.85 (0.14), residues: 1384 sheet: -0.55 (0.40), residues: 168 loop : -0.87 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 65 TYR 0.017 0.001 TYR A 812 PHE 0.012 0.001 PHE B 546 TRP 0.007 0.001 TRP D 578 HIS 0.003 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00292 (18456) covalent geometry : angle 0.47048 (24864) SS BOND : bond 0.00091 ( 8) SS BOND : angle 0.40532 ( 16) hydrogen bonds : bond 0.03899 ( 1131) hydrogen bonds : angle 3.34003 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8275 (mm) cc_final: 0.8011 (tp) REVERT: C 438 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8358 (mp) REVERT: C 439 GLU cc_start: 0.8286 (pt0) cc_final: 0.8049 (pt0) outliers start: 21 outliers final: 17 residues processed: 219 average time/residue: 0.1226 time to fit residues: 42.7873 Evaluate side-chains 209 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.102261 restraints weight = 21473.501| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.09 r_work: 0.2856 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 18464 Z= 0.272 Angle : 0.597 10.297 24880 Z= 0.307 Chirality : 0.043 0.162 2798 Planarity : 0.004 0.041 2992 Dihedral : 11.511 59.879 3406 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.01 % Allowed : 10.03 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.60 (0.18), residues: 2278 helix: 2.24 (0.13), residues: 1386 sheet: -0.64 (0.40), residues: 168 loop : -0.87 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 65 TYR 0.021 0.002 TYR D 702 PHE 0.015 0.002 PHE B 531 TRP 0.015 0.002 TRP B 578 HIS 0.008 0.002 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00658 (18456) covalent geometry : angle 0.59725 (24864) SS BOND : bond 0.00516 ( 8) SS BOND : angle 0.70886 ( 16) hydrogen bonds : bond 0.05068 ( 1131) hydrogen bonds : angle 3.73086 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.767 Fit side-chains REVERT: A 438 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 462 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: A 485 ILE cc_start: 0.8394 (mm) cc_final: 0.8155 (tp) REVERT: C 438 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 462 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7990 (mm-30) outliers start: 32 outliers final: 22 residues processed: 222 average time/residue: 0.1293 time to fit residues: 45.5253 Evaluate side-chains 212 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 chunk 92 optimal weight: 0.2980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107839 restraints weight = 21067.615| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.04 r_work: 0.2949 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18464 Z= 0.100 Angle : 0.460 9.255 24880 Z= 0.237 Chirality : 0.038 0.159 2798 Planarity : 0.003 0.043 2992 Dihedral : 9.939 59.226 3406 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.57 % Allowed : 11.03 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.18), residues: 2278 helix: 2.74 (0.14), residues: 1386 sheet: -0.52 (0.40), residues: 168 loop : -0.84 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 65 TYR 0.016 0.001 TYR A 812 PHE 0.009 0.001 PHE I 130 TRP 0.009 0.001 TRP J 203 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00214 (18456) covalent geometry : angle 0.45960 (24864) SS BOND : bond 0.00263 ( 8) SS BOND : angle 0.46544 ( 16) hydrogen bonds : bond 0.03597 ( 1131) hydrogen bonds : angle 3.34999 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.659 Fit side-chains REVERT: A 438 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 462 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: C 462 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: E 93 LEU cc_start: 0.6694 (mp) cc_final: 0.6450 (mp) outliers start: 25 outliers final: 17 residues processed: 212 average time/residue: 0.1225 time to fit residues: 41.6883 Evaluate side-chains 207 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 187 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS C 431 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103640 restraints weight = 21393.220| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.15 r_work: 0.2917 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18464 Z= 0.168 Angle : 0.510 9.220 24880 Z= 0.262 Chirality : 0.039 0.167 2798 Planarity : 0.003 0.042 2992 Dihedral : 10.336 57.041 3406 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.88 % Allowed : 11.28 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.96 (0.18), residues: 2278 helix: 2.56 (0.14), residues: 1388 sheet: -0.60 (0.40), residues: 168 loop : -0.81 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 65 TYR 0.014 0.001 TYR C 812 PHE 0.015 0.002 PHE D 546 TRP 0.010 0.001 TRP B 578 HIS 0.004 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00400 (18456) covalent geometry : angle 0.51001 (24864) SS BOND : bond 0.00208 ( 8) SS BOND : angle 0.57867 ( 16) hydrogen bonds : bond 0.04276 ( 1131) hydrogen bonds : angle 3.46170 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.659 Fit side-chains REVERT: A 438 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 462 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: B 508 GLN cc_start: 0.7594 (mt0) cc_final: 0.7311 (pm20) REVERT: C 438 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8375 (mp) REVERT: C 462 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: E 93 LEU cc_start: 0.6667 (mp) cc_final: 0.6420 (mp) outliers start: 30 outliers final: 23 residues processed: 213 average time/residue: 0.1219 time to fit residues: 41.5444 Evaluate side-chains 213 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 93 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.103516 restraints weight = 21299.032| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.98 r_work: 0.2938 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18464 Z= 0.124 Angle : 0.476 8.672 24880 Z= 0.244 Chirality : 0.038 0.165 2798 Planarity : 0.003 0.041 2992 Dihedral : 9.903 58.340 3406 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 11.78 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.18), residues: 2278 helix: 2.70 (0.14), residues: 1388 sheet: -0.65 (0.39), residues: 168 loop : -0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 65 TYR 0.015 0.001 TYR A 812 PHE 0.016 0.001 PHE B 546 TRP 0.007 0.001 TRP B 578 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00283 (18456) covalent geometry : angle 0.47588 (24864) SS BOND : bond 0.00153 ( 8) SS BOND : angle 0.79462 ( 16) hydrogen bonds : bond 0.03855 ( 1131) hydrogen bonds : angle 3.35138 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 438 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 508 GLN cc_start: 0.7607 (mt0) cc_final: 0.7400 (pm20) REVERT: C 438 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 462 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: E 93 LEU cc_start: 0.6679 (mp) cc_final: 0.6427 (mp) outliers start: 30 outliers final: 21 residues processed: 223 average time/residue: 0.1215 time to fit residues: 43.7457 Evaluate side-chains 224 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 0.3980 chunk 207 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110897 restraints weight = 21125.335| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.81 r_work: 0.2969 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18464 Z= 0.114 Angle : 0.471 8.397 24880 Z= 0.241 Chirality : 0.038 0.167 2798 Planarity : 0.003 0.041 2992 Dihedral : 9.602 58.980 3406 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.82 % Allowed : 11.72 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.18), residues: 2278 helix: 2.79 (0.14), residues: 1388 sheet: -0.74 (0.38), residues: 168 loop : -0.75 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 65 TYR 0.015 0.001 TYR A 812 PHE 0.014 0.001 PHE B 546 TRP 0.006 0.001 TRP B 578 HIS 0.003 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00257 (18456) covalent geometry : angle 0.47081 (24864) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.91927 ( 16) hydrogen bonds : bond 0.03729 ( 1131) hydrogen bonds : angle 3.30080 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 438 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8595 (mp) REVERT: E 93 LEU cc_start: 0.6694 (mp) cc_final: 0.6432 (mp) outliers start: 29 outliers final: 25 residues processed: 225 average time/residue: 0.1144 time to fit residues: 41.3468 Evaluate side-chains 231 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain E residue 19 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 202 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.157020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104015 restraints weight = 21301.388| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.09 r_work: 0.2909 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18464 Z= 0.167 Angle : 0.514 8.521 24880 Z= 0.263 Chirality : 0.039 0.168 2798 Planarity : 0.003 0.042 2992 Dihedral : 10.184 57.990 3406 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 11.65 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.98 (0.18), residues: 2278 helix: 2.58 (0.14), residues: 1388 sheet: -0.77 (0.38), residues: 168 loop : -0.74 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 65 TYR 0.014 0.001 TYR D 702 PHE 0.016 0.002 PHE B 546 TRP 0.009 0.001 TRP B 578 HIS 0.005 0.001 HIS I 83 Details of bonding type rmsd covalent geometry : bond 0.00398 (18456) covalent geometry : angle 0.51348 (24864) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.00708 ( 16) hydrogen bonds : bond 0.04258 ( 1131) hydrogen bonds : angle 3.44958 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4556 Ramachandran restraints generated. 2278 Oldfield, 0 Emsley, 2278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.639 Fit side-chains REVERT: A 438 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 462 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: C 438 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 462 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: E 93 LEU cc_start: 0.6682 (mp) cc_final: 0.6441 (mp) outliers start: 30 outliers final: 24 residues processed: 215 average time/residue: 0.1183 time to fit residues: 41.1365 Evaluate side-chains 219 residues out of total 1958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 27 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN I 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.154866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.104080 restraints weight = 21452.469| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.95 r_work: 0.2881 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18464 Z= 0.243 Angle : 0.585 9.382 24880 Z= 0.300 Chirality : 0.042 0.191 2798 Planarity : 0.004 0.043 2992 Dihedral : 10.968 59.520 3406 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.01 % Allowed : 11.72 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.58 (0.18), residues: 2278 helix: 2.22 (0.14), residues: 1388 sheet: -0.90 (0.38), residues: 168 loop : -0.83 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 65 TYR 0.019 0.002 TYR D 702 PHE 0.018 0.002 PHE B 546 TRP 0.014 0.002 TRP B 578 HIS 0.007 0.002 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00589 (18456) covalent geometry : angle 0.58435 (24864) SS BOND : bond 0.00277 ( 8) SS BOND : angle 1.07738 ( 16) hydrogen bonds : bond 0.04857 ( 1131) hydrogen bonds : angle 3.69143 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5614.16 seconds wall clock time: 96 minutes 29.96 seconds (5789.96 seconds total)