Starting phenix.real_space_refine on Mon Aug 25 22:26:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e4z_47521/08_2025/9e4z_47521.map" } resolution = 3.7 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 20049 2.51 5 N 5139 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31168 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 772} Chain breaks: 1 Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6257 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 772} Chain breaks: 1 Chain: "D" Number of atoms: 6253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6253 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1496 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CYZ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CYZ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 8.35, per 1000 atoms: 0.27 Number of scatterers: 31168 At special positions: 0 Unit cell: (115.32, 165.54, 193.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5804 8.00 N 5139 7.00 C 20049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E1039 " - pdb=" SG CYS E1067 " distance=2.03 Simple disulfide: pdb=" SG CYS E1066 " - pdb=" SG CYS E1076 " distance=2.04 Simple disulfide: pdb=" SG CYS F1039 " - pdb=" SG CYS F1067 " distance=2.03 Simple disulfide: pdb=" SG CYS F1066 " - pdb=" SG CYS F1076 " distance=2.04 Simple disulfide: pdb=" SG CYS G1039 " - pdb=" SG CYS G1067 " distance=2.02 Simple disulfide: pdb=" SG CYS G1066 " - pdb=" SG CYS G1076 " distance=2.04 Simple disulfide: pdb=" SG CYS H1039 " - pdb=" SG CYS H1067 " distance=2.03 Simple disulfide: pdb=" SG CYS H1066 " - pdb=" SG CYS H1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7252 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 36 sheets defined 51.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.520A pdb=" N ALA A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.769A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.900A pdb=" N LYS A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.563A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.604A pdb=" N ASN A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.890A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.661A pdb=" N PHE A 237 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.521A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 Processing helix chain 'A' and resid 572 through 583 removed outlier: 4.036A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 4.144A pdb=" N THR A 617 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.776A pdb=" N ARG A 694 " --> pdb=" O VAL A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 removed outlier: 4.317A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.702A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.899A pdb=" N LYS A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 820 removed outlier: 4.976A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.505A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.621A pdb=" N LYS B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.915A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 removed outlier: 4.000A pdb=" N ASP B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 323 through 334 removed outlier: 4.038A pdb=" N VAL B 327 " --> pdb=" O TRP B 323 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.964A pdb=" N VAL B 539 " --> pdb=" O GLY B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.706A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 621 removed outlier: 3.550A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 625 removed outlier: 3.857A pdb=" N THR B 625 " --> pdb=" O ALA B 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 622 through 625' Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.521A pdb=" N LYS B 641 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN B 642 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 4.712A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 675 Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.899A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 removed outlier: 3.630A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 758 through 765 Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.768A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 813 " --> pdb=" O VAL B 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.503A pdb=" N ALA C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.933A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.815A pdb=" N LYS C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.578A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.516A pdb=" N ASN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.717A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.078A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.572A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 543 Processing helix chain 'C' and resid 565 through 569 Processing helix chain 'C' and resid 572 through 583 removed outlier: 3.772A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 624 removed outlier: 3.616A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 642 removed outlier: 3.751A pdb=" N GLN C 642 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.567A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.612A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 removed outlier: 3.564A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 818 removed outlier: 4.635A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.606A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.634A pdb=" N LYS D 173 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 removed outlier: 3.823A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.132A pdb=" N ASP D 203 " --> pdb=" O ASP D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 252 through 264 Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.907A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 392 removed outlier: 3.851A pdb=" N GLU D 391 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 392' Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 522 through 544 Processing helix chain 'D' and resid 572 through 585 removed outlier: 4.025A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 617 removed outlier: 3.600A pdb=" N VAL D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 624 removed outlier: 5.401A pdb=" N ALA D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 696 removed outlier: 4.211A pdb=" N ARG D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 removed outlier: 3.554A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.775A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 813 " --> pdb=" O VAL D 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 1006 through 1029 removed outlier: 4.176A pdb=" N LEU E1010 " --> pdb=" O GLY E1006 " (cutoff:3.500A) Processing helix chain 'E' and resid 1092 through 1103 Processing helix chain 'E' and resid 1104 through 1121 Processing helix chain 'E' and resid 1122 through 1125 Processing helix chain 'E' and resid 1132 through 1160 removed outlier: 3.924A pdb=" N SER E1136 " --> pdb=" O ASN E1132 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E1137 " --> pdb=" O ILE E1133 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY E1138 " --> pdb=" O ILE E1134 " (cutoff:3.500A) Processing helix chain 'E' and resid 1176 through 1209 removed outlier: 3.879A pdb=" N ASP E1202 " --> pdb=" O HIS E1198 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E1205 " --> pdb=" O ILE E1201 " (cutoff:3.500A) Processing helix chain 'F' and resid 1004 through 1029 removed outlier: 3.839A pdb=" N MET F1009 " --> pdb=" O ARG F1005 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F1010 " --> pdb=" O GLY F1006 " (cutoff:3.500A) Processing helix chain 'F' and resid 1091 through 1103 Processing helix chain 'F' and resid 1104 through 1121 removed outlier: 4.104A pdb=" N ILE F1108 " --> pdb=" O SER F1104 " (cutoff:3.500A) Processing helix chain 'F' and resid 1122 through 1125 Processing helix chain 'F' and resid 1132 through 1160 removed outlier: 3.511A pdb=" N GLY F1145 " --> pdb=" O PHE F1141 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1204 Processing helix chain 'F' and resid 1204 through 1209 Processing helix chain 'G' and resid 1006 through 1029 removed outlier: 4.234A pdb=" N LEU G1010 " --> pdb=" O GLY G1006 " (cutoff:3.500A) Processing helix chain 'G' and resid 1091 through 1102 removed outlier: 3.810A pdb=" N LEU G1097 " --> pdb=" O ALA G1093 " (cutoff:3.500A) Processing helix chain 'G' and resid 1104 through 1121 Processing helix chain 'G' and resid 1122 through 1125 Processing helix chain 'G' and resid 1132 through 1160 removed outlier: 3.937A pdb=" N SER G1136 " --> pdb=" O ASN G1132 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA G1137 " --> pdb=" O ILE G1133 " (cutoff:3.500A) Processing helix chain 'G' and resid 1176 through 1208 removed outlier: 3.571A pdb=" N GLY G1182 " --> pdb=" O SER G1178 " (cutoff:3.500A) Processing helix chain 'H' and resid 1007 through 1029 removed outlier: 4.018A pdb=" N LEU H1011 " --> pdb=" O VAL H1007 " (cutoff:3.500A) Processing helix chain 'H' and resid 1084 through 1090 removed outlier: 3.725A pdb=" N TYR H1088 " --> pdb=" O ASP H1085 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU H1089 " --> pdb=" O ALA H1086 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA H1090 " --> pdb=" O ASP H1087 " (cutoff:3.500A) Processing helix chain 'H' and resid 1091 through 1103 Processing helix chain 'H' and resid 1104 through 1121 removed outlier: 3.854A pdb=" N ILE H1108 " --> pdb=" O SER H1104 " (cutoff:3.500A) Processing helix chain 'H' and resid 1131 through 1159 Processing helix chain 'H' and resid 1176 through 1209 removed outlier: 4.032A pdb=" N ARG H1203 " --> pdb=" O MET H1199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 49 removed outlier: 4.094A pdb=" N ALA A 72 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.506A pdb=" N TYR A 135 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 163 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS A 132 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 192 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.840A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.530A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.967A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 730 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.893A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.246A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.246A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 164 removed outlier: 7.076A pdb=" N PHE B 133 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 364 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB7, first strand: chain 'B' and resid 496 through 497 removed outlier: 4.353A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.345A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 48 removed outlier: 4.046A pdb=" N ALA C 72 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.511A pdb=" N ILE C 163 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 192 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR C 220 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE C 245 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE C 222 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N LYS C 364 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.595A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 343 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AC4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AC6, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.019A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.744A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 48 removed outlier: 4.328A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.052A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 364 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 439 through 444 removed outlier: 3.602A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD3, first strand: chain 'D' and resid 489 through 498 removed outlier: 4.816A pdb=" N ILE D 734 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR D 732 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET D 496 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS D 730 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.232A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 1056 through 1060 Processing sheet with id=AD6, first strand: chain 'E' and resid 1064 through 1065 Processing sheet with id=AD7, first strand: chain 'F' and resid 1077 through 1078 removed outlier: 3.550A pdb=" N SER F1060 " --> pdb=" O LEU F1033 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 1077 through 1078 removed outlier: 4.160A pdb=" N MET G1057 " --> pdb=" O LEU G1068 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 1077 through 1078 removed outlier: 3.675A pdb=" N SER H1060 " --> pdb=" O LEU H1033 " (cutoff:3.500A) 1574 hydrogen bonds defined for protein. 4473 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: 7.80 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.46: 15857 1.46 - 1.89: 15977 1.89 - 2.31: 4 2.31 - 2.74: 1 2.74 - 3.17: 1 Bond restraints: 31840 Sorted by residual: bond pdb=" CD LYS A 188 " pdb=" CE LYS A 188 " ideal model delta sigma weight residual 1.520 3.171 -1.651 3.00e-02 1.11e+03 3.03e+03 bond pdb=" CE LYS C 188 " pdb=" NZ LYS C 188 " ideal model delta sigma weight residual 1.489 2.723 -1.234 3.00e-02 1.11e+03 1.69e+03 bond pdb=" C4 CYZ B1303 " pdb=" C5 CYZ B1303 " ideal model delta sigma weight residual 1.512 1.030 0.482 2.00e-02 2.50e+03 5.80e+02 bond pdb=" C4 CYZ A1302 " pdb=" C5 CYZ A1302 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.78e+02 bond pdb=" C4 CYZ B1302 " pdb=" C5 CYZ B1302 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.77e+02 ... (remaining 31835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 42943 5.16 - 10.32: 65 10.32 - 15.48: 11 15.48 - 20.64: 14 20.64 - 25.79: 1 Bond angle restraints: 43034 Sorted by residual: angle pdb=" CG LYS A 188 " pdb=" CD LYS A 188 " pdb=" CE LYS A 188 " ideal model delta sigma weight residual 111.30 137.09 -25.79 2.30e+00 1.89e-01 1.26e+02 angle pdb=" C GLN A 586 " pdb=" CA GLN A 586 " pdb=" CB GLN A 586 " ideal model delta sigma weight residual 111.89 124.40 -12.51 1.42e+00 4.96e-01 7.77e+01 angle pdb=" N GLN D 586 " pdb=" CA GLN D 586 " pdb=" CB GLN D 586 " ideal model delta sigma weight residual 111.62 124.19 -12.57 1.43e+00 4.89e-01 7.73e+01 angle pdb=" C1 CYZ B1302 " pdb=" C2 CYZ B1302 " pdb=" C3 CYZ B1302 " ideal model delta sigma weight residual 106.92 126.81 -19.89 3.00e+00 1.11e-01 4.40e+01 angle pdb=" C1 CYZ A1303 " pdb=" C2 CYZ A1303 " pdb=" C3 CYZ A1303 " ideal model delta sigma weight residual 106.92 126.66 -19.74 3.00e+00 1.11e-01 4.33e+01 ... (remaining 43029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 18151 25.05 - 50.10: 608 50.10 - 75.15: 79 75.15 - 100.20: 28 100.20 - 125.25: 8 Dihedral angle restraints: 18874 sinusoidal: 7516 harmonic: 11358 Sorted by residual: dihedral pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" N GLU C 391 " pdb=" CA GLU C 391 " ideal model delta harmonic sigma weight residual -180.00 -126.34 -53.66 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual -86.00 -175.91 89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 172.93 -79.93 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 18871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.430: 4757 0.430 - 0.859: 9 0.859 - 1.289: 0 1.289 - 1.719: 0 1.719 - 2.148: 8 Chirality restraints: 4774 Sorted by residual: chirality pdb=" C5 CYZ B1302 " pdb=" C4 CYZ B1302 " pdb=" C6 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 1.16 2.15 2.00e-01 2.50e+01 1.15e+02 chirality pdb=" C5 CYZ A1302 " pdb=" C4 CYZ A1302 " pdb=" C6 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 1.16 2.14 2.00e-01 2.50e+01 1.15e+02 chirality pdb=" C5 CYZ A1303 " pdb=" C4 CYZ A1303 " pdb=" C6 CYZ A1303 " pdb=" C7 CYZ A1303 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 ... (remaining 4771 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 586 " -0.027 2.00e-02 2.50e+03 5.67e-02 3.22e+01 pdb=" CD GLN D 586 " 0.098 2.00e-02 2.50e+03 pdb=" OE1 GLN D 586 " -0.038 2.00e-02 2.50e+03 pdb=" NE2 GLN D 586 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 178 " 0.362 9.50e-02 1.11e+02 1.63e-01 2.08e+01 pdb=" NE ARG D 178 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 178 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG D 178 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG D 178 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 661 " -0.310 9.50e-02 1.11e+02 1.40e-01 1.52e+01 pdb=" NE ARG A 661 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 661 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 661 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 661 " -0.000 2.00e-02 2.50e+03 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 332 2.59 - 3.17: 28153 3.17 - 3.74: 48903 3.74 - 4.32: 69390 4.32 - 4.90: 111173 Nonbonded interactions: 257951 Sorted by model distance: nonbonded pdb=" NZ LYS C 188 " pdb=" CE2 TYR C 469 " model vdw 2.009 3.420 nonbonded pdb=" NZ LYS C 188 " pdb=" CZ TYR C 469 " model vdw 2.015 3.340 nonbonded pdb=" NZ LYS C 188 " pdb=" CE1 TYR C 469 " model vdw 2.017 3.420 nonbonded pdb=" NZ LYS C 188 " pdb=" CD2 TYR C 469 " model vdw 2.019 3.420 nonbonded pdb=" NZ LYS C 188 " pdb=" CD1 TYR C 469 " model vdw 2.026 3.420 ... (remaining 257946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 1301)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.760 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.740 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 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 : 0.019 1.651 31858 Z= 0.805 Angle : 0.803 25.794 43066 Z= 0.411 Chirality : 0.097 2.148 4774 Planarity : 0.008 0.163 5408 Dihedral : 13.736 125.255 11574 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.54 % Favored : 92.38 % Rotamer: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.53 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.12 (0.12), residues: 3910 helix: -1.35 (0.10), residues: 1804 sheet: -1.55 (0.24), residues: 397 loop : -1.24 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.003 ARG E1203 TYR 0.035 0.003 TYR F1095 PHE 0.021 0.002 PHE D 546 TRP 0.056 0.002 TRP C 323 HIS 0.016 0.001 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.01916 (31840) covalent geometry : angle 0.80151 (43034) SS BOND : bond 0.00445 ( 16) SS BOND : angle 2.11497 ( 32) hydrogen bonds : bond 0.16847 ( 1574) hydrogen bonds : angle 7.54040 ( 4473) Misc. bond : bond 0.00572 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 847 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7245 (tmt170) cc_final: 0.6696 (ptt-90) REVERT: A 199 ASP cc_start: 0.7790 (m-30) cc_final: 0.7077 (t0) REVERT: A 294 GLU cc_start: 0.6561 (tp30) cc_final: 0.6211 (tm-30) REVERT: A 361 MET cc_start: 0.7447 (mmm) cc_final: 0.6538 (mmm) REVERT: A 435 HIS cc_start: 0.7044 (t-90) cc_final: 0.5699 (m-70) REVERT: A 531 PHE cc_start: 0.7357 (m-10) cc_final: 0.7045 (m-10) REVERT: A 814 PHE cc_start: 0.6930 (t80) cc_final: 0.6317 (t80) REVERT: B 167 ASN cc_start: 0.7749 (m-40) cc_final: 0.7433 (m-40) REVERT: B 629 MET cc_start: 0.4302 (tmm) cc_final: 0.3556 (tpp) REVERT: C 198 ARG cc_start: 0.7298 (tmt170) cc_final: 0.6767 (ptt-90) REVERT: C 357 THR cc_start: 0.8631 (m) cc_final: 0.8346 (p) REVERT: C 497 SER cc_start: 0.8807 (m) cc_final: 0.8587 (t) REVERT: C 527 MET cc_start: 0.8115 (ttm) cc_final: 0.7783 (ttm) REVERT: C 531 PHE cc_start: 0.7044 (m-10) cc_final: 0.6782 (m-80) REVERT: C 574 PHE cc_start: 0.8561 (t80) cc_final: 0.8343 (t80) REVERT: C 683 VAL cc_start: 0.7717 (m) cc_final: 0.7495 (t) REVERT: C 708 MET cc_start: 0.6080 (mmt) cc_final: 0.5058 (tpp) REVERT: C 812 ILE cc_start: 0.7937 (pt) cc_final: 0.7692 (mt) REVERT: D 286 TYR cc_start: 0.6810 (t80) cc_final: 0.6032 (t80) REVERT: D 521 LEU cc_start: 0.8729 (mp) cc_final: 0.8501 (mt) REVERT: E 1009 MET cc_start: 0.8494 (tpt) cc_final: 0.7957 (tpp) REVERT: E 1059 HIS cc_start: 0.6683 (t-170) cc_final: 0.6435 (t-170) REVERT: E 1095 TYR cc_start: 0.7843 (t80) cc_final: 0.7627 (t80) REVERT: E 1191 MET cc_start: 0.8381 (mmm) cc_final: 0.8167 (mmt) REVERT: G 1009 MET cc_start: 0.8125 (tpt) cc_final: 0.7747 (tpp) REVERT: G 1174 SER cc_start: 0.7872 (t) cc_final: 0.7643 (m) REVERT: H 1004 ASP cc_start: 0.6279 (m-30) cc_final: 0.5739 (m-30) REVERT: H 1126 PHE cc_start: 0.5977 (t80) cc_final: 0.5426 (m-10) REVERT: H 1139 ILE cc_start: 0.8227 (mm) cc_final: 0.7808 (mm) outliers start: 4 outliers final: 1 residues processed: 849 average time/residue: 0.2359 time to fit residues: 309.4522 Evaluate side-chains 461 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 620 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 246 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN B 619 ASN C 46 HIS D 54 ASN D 167 ASN D 714 GLN ** E1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1159 ASN G1008 GLN G1081 HIS G1148 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.194948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163895 restraints weight = 54061.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164348 restraints weight = 78173.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165332 restraints weight = 74581.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.166986 restraints weight = 47034.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168130 restraints weight = 38504.942| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.666 31858 Z= 0.539 Angle : 0.722 24.205 43066 Z= 0.378 Chirality : 0.045 0.288 4774 Planarity : 0.005 0.064 5408 Dihedral : 8.086 102.177 4390 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.94 % Favored : 94.99 % Rotamer: Outliers : 2.22 % Allowed : 11.83 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.90 (0.13), residues: 3910 helix: 0.08 (0.12), residues: 1861 sheet: -1.21 (0.26), residues: 355 loop : -1.13 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H1064 TYR 0.032 0.002 TYR G1088 PHE 0.034 0.002 PHE G1141 TRP 0.030 0.002 TRP E1032 HIS 0.009 0.002 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.01510 (31840) covalent geometry : angle 0.72133 (43034) SS BOND : bond 0.00414 ( 16) SS BOND : angle 1.25931 ( 32) hydrogen bonds : bond 0.04944 ( 1574) hydrogen bonds : angle 5.41656 ( 4473) Misc. bond : bond 0.00502 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 536 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ARG cc_start: 0.7104 (tmt170) cc_final: 0.6876 (ptt-90) REVERT: A 199 ASP cc_start: 0.7506 (m-30) cc_final: 0.7016 (t0) REVERT: A 361 MET cc_start: 0.7757 (mmm) cc_final: 0.7329 (mmt) REVERT: A 435 HIS cc_start: 0.6885 (t-90) cc_final: 0.5671 (m-70) REVERT: A 527 MET cc_start: 0.7854 (ttm) cc_final: 0.7335 (ttm) REVERT: A 531 PHE cc_start: 0.7274 (m-10) cc_final: 0.6969 (m-10) REVERT: A 670 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (mtm) REVERT: B 629 MET cc_start: 0.4336 (tmm) cc_final: 0.3659 (tpp) REVERT: B 816 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4766 (m-80) REVERT: C 156 LYS cc_start: 0.7640 (mppt) cc_final: 0.7360 (mtmt) REVERT: C 198 ARG cc_start: 0.7061 (tmt170) cc_final: 0.6597 (ttt-90) REVERT: C 298 ASN cc_start: 0.7369 (t0) cc_final: 0.7081 (t0) REVERT: C 527 MET cc_start: 0.7863 (ttm) cc_final: 0.7590 (ttm) REVERT: C 531 PHE cc_start: 0.7111 (m-10) cc_final: 0.6887 (m-80) REVERT: C 812 ILE cc_start: 0.8132 (pt) cc_final: 0.7911 (mt) REVERT: D 195 ASP cc_start: 0.8416 (t0) cc_final: 0.8004 (t0) REVERT: D 485 ARG cc_start: 0.6916 (mtm-85) cc_final: 0.6715 (mtm-85) REVERT: D 577 LEU cc_start: 0.8229 (mt) cc_final: 0.8015 (mt) REVERT: E 1199 MET cc_start: 0.7900 (mtp) cc_final: 0.7583 (ttm) REVERT: F 1112 ILE cc_start: 0.6551 (OUTLIER) cc_final: 0.6269 (pt) REVERT: G 1199 MET cc_start: 0.7725 (mtp) cc_final: 0.7189 (ttm) REVERT: H 1139 ILE cc_start: 0.8302 (mm) cc_final: 0.7919 (mm) outliers start: 74 outliers final: 46 residues processed: 579 average time/residue: 0.2184 time to fit residues: 199.5401 Evaluate side-chains 473 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 424 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 816 TYR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 787 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain E residue 1111 VAL Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1110 SER Chi-restraints excluded: chain F residue 1112 ILE Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain G residue 1081 HIS Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1149 ILE Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1056 VAL Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 196 optimal weight: 0.0970 chunk 121 optimal weight: 0.3980 chunk 276 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 331 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 206 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 283 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 167 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 325 GLN D 435 HIS E1008 GLN ** E1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1204 HIS G1008 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.196689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164061 restraints weight = 53275.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164383 restraints weight = 79217.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.165933 restraints weight = 66829.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.166638 restraints weight = 43151.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.169385 restraints weight = 36156.066| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.667 31858 Z= 0.535 Angle : 0.684 23.356 43066 Z= 0.356 Chirality : 0.044 0.253 4774 Planarity : 0.004 0.056 5408 Dihedral : 7.580 93.504 4388 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 2.79 % Allowed : 14.68 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.66 (0.13), residues: 3910 helix: 0.45 (0.12), residues: 1877 sheet: -1.30 (0.25), residues: 388 loop : -1.20 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1098 TYR 0.055 0.002 TYR G1127 PHE 0.038 0.002 PHE G1141 TRP 0.039 0.002 TRP E1032 HIS 0.010 0.001 HIS E1059 Details of bonding type rmsd covalent geometry : bond 0.01503 (31840) covalent geometry : angle 0.68238 (43034) SS BOND : bond 0.00660 ( 16) SS BOND : angle 2.01414 ( 32) hydrogen bonds : bond 0.04441 ( 1574) hydrogen bonds : angle 5.09625 ( 4473) Misc. bond : bond 0.00440 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 477 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7518 (m-30) cc_final: 0.7039 (t0) REVERT: A 207 GLN cc_start: 0.8030 (mm110) cc_final: 0.7738 (tp40) REVERT: A 435 HIS cc_start: 0.6637 (t-90) cc_final: 0.5634 (m-70) REVERT: A 531 PHE cc_start: 0.7346 (m-10) cc_final: 0.7042 (m-10) REVERT: B 33 MET cc_start: 0.5697 (tpt) cc_final: 0.5209 (tpt) REVERT: B 218 TYR cc_start: 0.7587 (m-80) cc_final: 0.7312 (m-80) REVERT: B 629 MET cc_start: 0.4346 (tmm) cc_final: 0.3664 (tpp) REVERT: C 187 LYS cc_start: 0.5687 (mttt) cc_final: 0.5332 (tptm) REVERT: C 198 ARG cc_start: 0.7018 (tmt170) cc_final: 0.6576 (ttt-90) REVERT: C 298 ASN cc_start: 0.7416 (t0) cc_final: 0.7097 (t0) REVERT: C 527 MET cc_start: 0.7929 (ttm) cc_final: 0.7670 (ttm) REVERT: C 531 PHE cc_start: 0.7247 (m-10) cc_final: 0.7001 (m-80) REVERT: C 620 LEU cc_start: 0.8395 (tt) cc_final: 0.8139 (tt) REVERT: C 705 GLU cc_start: 0.7224 (pm20) cc_final: 0.6738 (pm20) REVERT: C 710 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: C 812 ILE cc_start: 0.8083 (pt) cc_final: 0.7842 (mt) REVERT: D 198 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7374 (tpp-160) REVERT: D 577 LEU cc_start: 0.8245 (mt) cc_final: 0.8018 (mt) REVERT: E 1199 MET cc_start: 0.8093 (mtp) cc_final: 0.7718 (ttm) REVERT: G 1020 PHE cc_start: 0.7815 (t80) cc_final: 0.7507 (t80) REVERT: G 1057 MET cc_start: 0.7019 (mpp) cc_final: 0.6344 (mpp) REVERT: G 1081 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6187 (t-90) REVERT: H 1022 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5069 (mm) REVERT: H 1064 ARG cc_start: 0.6236 (mpt180) cc_final: 0.5329 (mtm-85) REVERT: H 1139 ILE cc_start: 0.8132 (mm) cc_final: 0.7826 (mm) outliers start: 93 outliers final: 59 residues processed: 536 average time/residue: 0.2190 time to fit residues: 187.4215 Evaluate side-chains 485 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 423 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1007 VAL Chi-restraints excluded: chain E residue 1111 VAL Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1110 SER Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain G residue 1081 HIS Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1110 SER Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 379 optimal weight: 0.0170 chunk 98 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 236 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 283 optimal weight: 0.1980 chunk 308 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 412 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS D 435 HIS D 791 ASN H1008 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.196272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.164671 restraints weight = 53583.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.165473 restraints weight = 74774.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.166459 restraints weight = 67426.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.167725 restraints weight = 42511.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.169207 restraints weight = 35873.149| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.667 31858 Z= 0.525 Angle : 0.645 22.814 43066 Z= 0.333 Chirality : 0.043 0.248 4774 Planarity : 0.004 0.059 5408 Dihedral : 7.027 89.986 4388 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.04 % Favored : 95.88 % Rotamer: Outliers : 3.08 % Allowed : 15.24 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.39 (0.13), residues: 3910 helix: 0.75 (0.12), residues: 1889 sheet: -1.25 (0.25), residues: 388 loop : -1.15 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G1064 TYR 0.026 0.001 TYR G1088 PHE 0.041 0.002 PHE G1141 TRP 0.050 0.002 TRP E1032 HIS 0.015 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.01482 (31840) covalent geometry : angle 0.64317 (43034) SS BOND : bond 0.00707 ( 16) SS BOND : angle 1.90718 ( 32) hydrogen bonds : bond 0.03951 ( 1574) hydrogen bonds : angle 4.81955 ( 4473) Misc. bond : bond 0.00349 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 503 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7201 (m-30) cc_final: 0.6983 (t0) REVERT: A 207 GLN cc_start: 0.8008 (mm110) cc_final: 0.7718 (tp40) REVERT: A 361 MET cc_start: 0.7497 (mmm) cc_final: 0.7137 (mmm) REVERT: A 435 HIS cc_start: 0.6641 (t-90) cc_final: 0.5658 (m-70) REVERT: A 531 PHE cc_start: 0.7148 (m-10) cc_final: 0.6882 (m-10) REVERT: A 798 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6526 (tt) REVERT: B 629 MET cc_start: 0.4177 (tmm) cc_final: 0.3717 (tpp) REVERT: C 198 ARG cc_start: 0.6935 (tmt170) cc_final: 0.6588 (ttt-90) REVERT: C 199 ASP cc_start: 0.7451 (m-30) cc_final: 0.6872 (t0) REVERT: C 298 ASN cc_start: 0.7411 (t0) cc_final: 0.7065 (t0) REVERT: C 527 MET cc_start: 0.7842 (ttm) cc_final: 0.7629 (ttm) REVERT: C 531 PHE cc_start: 0.7215 (m-10) cc_final: 0.6971 (m-80) REVERT: C 620 LEU cc_start: 0.8366 (tt) cc_final: 0.8062 (tt) REVERT: C 812 ILE cc_start: 0.8029 (pt) cc_final: 0.7770 (mt) REVERT: D 195 ASP cc_start: 0.8553 (t0) cc_final: 0.8168 (t0) REVERT: D 198 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7409 (tpp-160) REVERT: D 463 MET cc_start: 0.7823 (tpp) cc_final: 0.7548 (mmt) REVERT: D 485 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6512 (mtm-85) REVERT: E 1199 MET cc_start: 0.8024 (mtp) cc_final: 0.7655 (ttm) REVERT: G 1020 PHE cc_start: 0.7700 (t80) cc_final: 0.7489 (t80) REVERT: G 1057 MET cc_start: 0.6851 (mpp) cc_final: 0.6198 (mpp) REVERT: G 1063 TRP cc_start: 0.6439 (t60) cc_final: 0.5879 (t60) REVERT: G 1155 TYR cc_start: 0.7284 (t80) cc_final: 0.7081 (t80) REVERT: H 1022 LEU cc_start: 0.5264 (OUTLIER) cc_final: 0.5014 (mm) REVERT: H 1127 TYR cc_start: 0.6748 (t80) cc_final: 0.6226 (t80) REVERT: H 1139 ILE cc_start: 0.8057 (mm) cc_final: 0.7769 (mm) REVERT: H 1191 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7782 (ttm) outliers start: 103 outliers final: 60 residues processed: 568 average time/residue: 0.2204 time to fit residues: 198.5400 Evaluate side-chains 492 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 429 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain E residue 1007 VAL Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1081 HIS Chi-restraints excluded: chain G residue 1192 VAL Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1194 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 120 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 377 optimal weight: 20.0000 chunk 350 optimal weight: 10.0000 chunk 347 optimal weight: 0.4980 chunk 357 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 325 GLN B 54 ASN B 93 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS D 93 HIS D 435 HIS E1008 GLN ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1132 ASN ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1008 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.187990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154551 restraints weight = 53741.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158555 restraints weight = 86191.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158660 restraints weight = 61105.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.159370 restraints weight = 44936.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161784 restraints weight = 36630.670| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.676 31858 Z= 0.598 Angle : 0.808 23.996 43066 Z= 0.421 Chirality : 0.050 0.241 4774 Planarity : 0.005 0.057 5408 Dihedral : 7.022 85.057 4388 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.75 % Favored : 94.14 % Rotamer: Outliers : 4.49 % Allowed : 16.71 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.98 (0.13), residues: 3910 helix: 0.26 (0.12), residues: 1870 sheet: -1.64 (0.24), residues: 398 loop : -1.38 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G1098 TYR 0.053 0.002 TYR G1127 PHE 0.040 0.003 PHE C 29 TRP 0.049 0.003 TRP E1032 HIS 0.016 0.002 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.01636 (31840) covalent geometry : angle 0.80623 (43034) SS BOND : bond 0.00637 ( 16) SS BOND : angle 1.94700 ( 32) hydrogen bonds : bond 0.04967 ( 1574) hydrogen bonds : angle 5.31430 ( 4473) Misc. bond : bond 0.00670 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 471 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7473 (m-30) cc_final: 0.7011 (t0) REVERT: A 361 MET cc_start: 0.7795 (mmm) cc_final: 0.7521 (mmm) REVERT: A 435 HIS cc_start: 0.6707 (t-90) cc_final: 0.5401 (m-70) REVERT: A 531 PHE cc_start: 0.7504 (m-10) cc_final: 0.7204 (m-10) REVERT: B 414 MET cc_start: 0.7343 (ppp) cc_final: 0.6841 (pmm) REVERT: B 463 MET cc_start: 0.7238 (mmt) cc_final: 0.6862 (mmt) REVERT: B 568 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6518 (m) REVERT: B 751 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7271 (tt) REVERT: B 787 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 803 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7923 (mp) REVERT: C 97 ILE cc_start: 0.8349 (mp) cc_final: 0.8068 (mt) REVERT: C 198 ARG cc_start: 0.7133 (tmt170) cc_final: 0.6828 (ttt-90) REVERT: C 199 ASP cc_start: 0.7734 (m-30) cc_final: 0.7005 (t0) REVERT: C 298 ASN cc_start: 0.7558 (t0) cc_final: 0.7153 (t0) REVERT: C 527 MET cc_start: 0.8018 (ttm) cc_final: 0.7744 (ttm) REVERT: C 531 PHE cc_start: 0.7435 (m-10) cc_final: 0.7229 (m-80) REVERT: C 722 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8022 (ttpt) REVERT: C 812 ILE cc_start: 0.8110 (pt) cc_final: 0.7874 (mt) REVERT: D 195 ASP cc_start: 0.8753 (t0) cc_final: 0.8388 (t0) REVERT: D 586 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8142 (mm110) REVERT: E 1021 SER cc_start: 0.8845 (m) cc_final: 0.8471 (p) REVERT: E 1155 TYR cc_start: 0.7416 (t80) cc_final: 0.6999 (t80) REVERT: G 1005 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7529 (mtp85) REVERT: G 1057 MET cc_start: 0.6812 (mpp) cc_final: 0.6134 (mpp) REVERT: H 1022 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.5005 (mm) REVERT: H 1127 TYR cc_start: 0.6814 (t80) cc_final: 0.6356 (t80) REVERT: H 1139 ILE cc_start: 0.8047 (mm) cc_final: 0.7744 (mm) outliers start: 150 outliers final: 113 residues processed: 578 average time/residue: 0.2103 time to fit residues: 196.0030 Evaluate side-chains 542 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 422 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 533 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 586 GLN Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1002 LEU Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain E residue 1194 VAL Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1110 SER Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1188 ILE Chi-restraints excluded: chain F residue 1191 MET Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1081 HIS Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1149 ILE Chi-restraints excluded: chain G residue 1192 VAL Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1032 TRP Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1056 VAL Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 49 optimal weight: 0.0060 chunk 16 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 380 optimal weight: 9.9990 chunk 307 optimal weight: 0.3980 chunk 387 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 190 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS D 435 HIS E1008 GLN ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1008 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.192487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.160025 restraints weight = 53347.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162009 restraints weight = 74951.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.162693 restraints weight = 66059.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.163287 restraints weight = 44667.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163660 restraints weight = 37362.614| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.662 31858 Z= 0.529 Angle : 0.673 22.902 43066 Z= 0.349 Chirality : 0.044 0.239 4774 Planarity : 0.004 0.053 5408 Dihedral : 6.768 86.744 4388 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.56 % Allowed : 19.41 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.60 (0.13), residues: 3910 helix: 0.66 (0.12), residues: 1896 sheet: -1.43 (0.25), residues: 402 loop : -1.35 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G1098 TYR 0.028 0.002 TYR G1088 PHE 0.044 0.002 PHE G1141 TRP 0.046 0.002 TRP C 671 HIS 0.015 0.001 HIS F1081 Details of bonding type rmsd covalent geometry : bond 0.01492 (31840) covalent geometry : angle 0.67017 (43034) SS BOND : bond 0.00747 ( 16) SS BOND : angle 2.28443 ( 32) hydrogen bonds : bond 0.04055 ( 1574) hydrogen bonds : angle 4.94986 ( 4473) Misc. bond : bond 0.00398 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 460 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6542 (t0) cc_final: 0.6098 (t0) REVERT: A 361 MET cc_start: 0.7875 (mmm) cc_final: 0.7541 (mmm) REVERT: A 435 HIS cc_start: 0.6676 (t-90) cc_final: 0.5665 (m-70) REVERT: A 531 PHE cc_start: 0.7205 (m-10) cc_final: 0.6950 (m-10) REVERT: A 683 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7453 (t) REVERT: B 414 MET cc_start: 0.7511 (ppp) cc_final: 0.7028 (pmm) REVERT: B 463 MET cc_start: 0.7342 (mmt) cc_final: 0.6808 (mmt) REVERT: B 568 THR cc_start: 0.6870 (OUTLIER) cc_final: 0.6541 (m) REVERT: B 578 TRP cc_start: 0.7494 (t-100) cc_final: 0.7207 (t-100) REVERT: B 629 MET cc_start: 0.4369 (ppp) cc_final: 0.3641 (tpp) REVERT: B 803 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8018 (mp) REVERT: C 97 ILE cc_start: 0.8301 (mp) cc_final: 0.7970 (mt) REVERT: C 198 ARG cc_start: 0.6998 (tmt170) cc_final: 0.6626 (ttt-90) REVERT: C 199 ASP cc_start: 0.7506 (m-30) cc_final: 0.6846 (t0) REVERT: C 298 ASN cc_start: 0.7442 (t0) cc_final: 0.7062 (t0) REVERT: C 620 LEU cc_start: 0.8431 (tt) cc_final: 0.8194 (tt) REVERT: C 812 ILE cc_start: 0.7983 (pt) cc_final: 0.7777 (mt) REVERT: D 195 ASP cc_start: 0.8646 (t0) cc_final: 0.8207 (t0) REVERT: D 463 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7419 (mmt) REVERT: E 1021 SER cc_start: 0.8823 (m) cc_final: 0.8536 (p) REVERT: E 1041 THR cc_start: 0.5120 (OUTLIER) cc_final: 0.4748 (p) REVERT: E 1155 TYR cc_start: 0.7294 (t80) cc_final: 0.6974 (t80) REVERT: E 1199 MET cc_start: 0.8074 (mtp) cc_final: 0.7599 (ttm) REVERT: F 1082 PHE cc_start: 0.6449 (p90) cc_final: 0.6006 (p90) REVERT: G 1033 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5229 (pp) REVERT: G 1063 TRP cc_start: 0.6321 (t60) cc_final: 0.5899 (t60) REVERT: G 1155 TYR cc_start: 0.7325 (t80) cc_final: 0.7084 (t80) REVERT: H 1022 LEU cc_start: 0.5128 (OUTLIER) cc_final: 0.4896 (mm) REVERT: H 1064 ARG cc_start: 0.6139 (mpt180) cc_final: 0.5302 (mtm-85) REVERT: H 1127 TYR cc_start: 0.6773 (t80) cc_final: 0.6514 (t80) REVERT: H 1139 ILE cc_start: 0.8059 (mm) cc_final: 0.7783 (mm) outliers start: 119 outliers final: 80 residues processed: 545 average time/residue: 0.2117 time to fit residues: 186.4047 Evaluate side-chains 494 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 407 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 672 THR Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1039 CYS Chi-restraints excluded: chain E residue 1041 THR Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1075 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1191 MET Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1033 LEU Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1159 ASN Chi-restraints excluded: chain G residue 1192 VAL Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1032 TRP Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1194 VAL Chi-restraints excluded: chain H residue 1197 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 151 optimal weight: 0.7980 chunk 389 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.192129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.159004 restraints weight = 53427.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162365 restraints weight = 87391.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.162976 restraints weight = 61821.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163658 restraints weight = 46632.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164810 restraints weight = 37517.534| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.230 31858 Z= 0.397 Angle : 0.709 19.711 43066 Z= 0.371 Chirality : 0.046 0.211 4774 Planarity : 0.004 0.053 5408 Dihedral : 6.652 84.698 4388 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 4.01 % Allowed : 19.71 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.75 (0.13), residues: 3910 helix: 0.58 (0.12), residues: 1886 sheet: -1.55 (0.25), residues: 390 loop : -1.47 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G1098 TYR 0.040 0.002 TYR G1127 PHE 0.046 0.002 PHE G1141 TRP 0.048 0.002 TRP D 323 HIS 0.009 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.01069 (31840) covalent geometry : angle 0.70659 (43034) SS BOND : bond 0.00699 ( 16) SS BOND : angle 2.25449 ( 32) hydrogen bonds : bond 0.04400 ( 1574) hydrogen bonds : angle 5.05325 ( 4473) Misc. bond : bond 0.00522 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 426 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 HIS cc_start: 0.6646 (t-90) cc_final: 0.5454 (m-70) REVERT: A 531 PHE cc_start: 0.7363 (m-10) cc_final: 0.7096 (m-10) REVERT: A 651 ASP cc_start: 0.8047 (t0) cc_final: 0.7746 (t0) REVERT: A 683 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7387 (t) REVERT: B 414 MET cc_start: 0.7574 (ppp) cc_final: 0.7151 (pmm) REVERT: B 463 MET cc_start: 0.7326 (mmt) cc_final: 0.6677 (mmt) REVERT: B 613 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 629 MET cc_start: 0.4709 (ppp) cc_final: 0.3926 (tpp) REVERT: B 721 MET cc_start: 0.7023 (ppp) cc_final: 0.6486 (ppp) REVERT: B 787 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 803 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7958 (mp) REVERT: C 97 ILE cc_start: 0.8322 (mp) cc_final: 0.8005 (mt) REVERT: C 145 THR cc_start: 0.8410 (p) cc_final: 0.8207 (t) REVERT: C 178 ARG cc_start: 0.6477 (ttp80) cc_final: 0.6111 (ttp80) REVERT: C 198 ARG cc_start: 0.7099 (tmt170) cc_final: 0.6727 (ttt-90) REVERT: C 199 ASP cc_start: 0.7619 (m-30) cc_final: 0.6933 (t0) REVERT: C 298 ASN cc_start: 0.7478 (t0) cc_final: 0.7088 (t0) REVERT: C 361 MET cc_start: 0.7750 (mmt) cc_final: 0.7201 (mmt) REVERT: C 812 ILE cc_start: 0.8066 (pt) cc_final: 0.7842 (mt) REVERT: D 195 ASP cc_start: 0.8661 (t0) cc_final: 0.8233 (t0) REVERT: D 463 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7352 (mmt) REVERT: E 1020 PHE cc_start: 0.7684 (t80) cc_final: 0.7433 (t80) REVERT: E 1021 SER cc_start: 0.8974 (m) cc_final: 0.8499 (p) REVERT: E 1148 ASN cc_start: 0.7990 (t0) cc_final: 0.7763 (t0) REVERT: E 1155 TYR cc_start: 0.7340 (t80) cc_final: 0.6979 (t80) REVERT: E 1199 MET cc_start: 0.7934 (mtp) cc_final: 0.7617 (ttm) REVERT: F 1173 TYR cc_start: 0.7205 (p90) cc_final: 0.6943 (p90) REVERT: G 1033 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5195 (pp) REVERT: G 1063 TRP cc_start: 0.6318 (t60) cc_final: 0.6063 (t60) REVERT: H 1022 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4900 (mm) REVERT: H 1064 ARG cc_start: 0.6218 (mpt180) cc_final: 0.5298 (mtm-85) REVERT: H 1127 TYR cc_start: 0.6717 (t80) cc_final: 0.6478 (t80) REVERT: H 1139 ILE cc_start: 0.8039 (mm) cc_final: 0.7755 (mm) REVERT: H 1191 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7755 (ttm) outliers start: 134 outliers final: 106 residues processed: 522 average time/residue: 0.2104 time to fit residues: 177.2581 Evaluate side-chains 515 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 401 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 380 MET Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 533 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1039 CYS Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1011 LEU Chi-restraints excluded: chain F residue 1109 LEU Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1033 LEU Chi-restraints excluded: chain G residue 1081 HIS Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1149 ILE Chi-restraints excluded: chain G residue 1192 VAL Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1032 TRP Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1188 ILE Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1194 VAL Chi-restraints excluded: chain H residue 1197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 15 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 373 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 330 optimal weight: 0.0980 chunk 282 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1204 HIS ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1008 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.192788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.162003 restraints weight = 53776.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162594 restraints weight = 80859.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163638 restraints weight = 72921.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.164896 restraints weight = 46320.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.166552 restraints weight = 38444.207| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.230 31858 Z= 0.356 Angle : 0.648 20.134 43066 Z= 0.338 Chirality : 0.043 0.203 4774 Planarity : 0.004 0.053 5408 Dihedral : 6.426 85.291 4388 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.65 % Rotamer: Outliers : 3.20 % Allowed : 20.69 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.45 (0.14), residues: 3910 helix: 0.83 (0.12), residues: 1903 sheet: -1.36 (0.25), residues: 397 loop : -1.36 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G1098 TYR 0.028 0.001 TYR A 26 PHE 0.043 0.002 PHE G1141 TRP 0.061 0.002 TRP E1032 HIS 0.008 0.001 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.00980 (31840) covalent geometry : angle 0.64616 (43034) SS BOND : bond 0.00729 ( 16) SS BOND : angle 2.06127 ( 32) hydrogen bonds : bond 0.03859 ( 1574) hydrogen bonds : angle 4.81647 ( 4473) Misc. bond : bond 0.00397 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 444 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.7600 (mmm) cc_final: 0.7397 (mmm) REVERT: A 435 HIS cc_start: 0.6548 (t-90) cc_final: 0.5428 (m-70) REVERT: A 531 PHE cc_start: 0.7205 (m-10) cc_final: 0.6991 (m-80) REVERT: B 463 MET cc_start: 0.7171 (mmt) cc_final: 0.6507 (mmt) REVERT: B 527 MET cc_start: 0.8064 (tpp) cc_final: 0.7845 (tpt) REVERT: B 629 MET cc_start: 0.4593 (ppp) cc_final: 0.3890 (tpp) REVERT: B 803 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7988 (mp) REVERT: C 97 ILE cc_start: 0.8258 (mp) cc_final: 0.7932 (mt) REVERT: C 198 ARG cc_start: 0.6902 (tmt170) cc_final: 0.6701 (ptt-90) REVERT: C 199 ASP cc_start: 0.7412 (m-30) cc_final: 0.6656 (t0) REVERT: C 298 ASN cc_start: 0.7472 (t0) cc_final: 0.7075 (t0) REVERT: C 361 MET cc_start: 0.7665 (mmt) cc_final: 0.7158 (mmt) REVERT: C 620 LEU cc_start: 0.8411 (tt) cc_final: 0.8170 (tt) REVERT: C 812 ILE cc_start: 0.8060 (pt) cc_final: 0.7830 (mt) REVERT: D 463 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7386 (mmt) REVERT: D 705 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7597 (mp0) REVERT: E 1021 SER cc_start: 0.8887 (m) cc_final: 0.8462 (p) REVERT: E 1148 ASN cc_start: 0.7806 (t0) cc_final: 0.7582 (t0) REVERT: E 1155 TYR cc_start: 0.7208 (t80) cc_final: 0.6920 (t80) REVERT: E 1199 MET cc_start: 0.7945 (mtp) cc_final: 0.7675 (ttm) REVERT: F 1173 TYR cc_start: 0.7096 (p90) cc_final: 0.6868 (p90) REVERT: G 1033 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5079 (pp) REVERT: G 1082 PHE cc_start: 0.4971 (p90) cc_final: 0.4606 (p90) REVERT: H 1022 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4856 (mm) REVERT: H 1064 ARG cc_start: 0.6100 (mpt180) cc_final: 0.5388 (mtm-85) REVERT: H 1127 TYR cc_start: 0.6847 (t80) cc_final: 0.6625 (t80) REVERT: H 1139 ILE cc_start: 0.8090 (mm) cc_final: 0.7818 (mm) REVERT: H 1191 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7490 (ttm) outliers start: 107 outliers final: 82 residues processed: 521 average time/residue: 0.2072 time to fit residues: 175.5972 Evaluate side-chains 498 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 411 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 722 LYS Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 323 TRP Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 670 MET Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1009 MET Chi-restraints excluded: chain E residue 1039 CYS Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1115 PHE Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1191 MET Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1033 LEU Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1105 ILE Chi-restraints excluded: chain H residue 1007 VAL Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1032 TRP Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1194 VAL Chi-restraints excluded: chain H residue 1197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 53 optimal weight: 2.9990 chunk 379 optimal weight: 0.9990 chunk 303 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 304 optimal weight: 0.9980 chunk 362 optimal weight: 0.6980 chunk 144 optimal weight: 0.0570 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1204 HIS ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.196675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165682 restraints weight = 53487.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.165852 restraints weight = 78073.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166865 restraints weight = 71914.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168120 restraints weight = 46332.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169926 restraints weight = 38369.178| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.231 31858 Z= 0.355 Angle : 0.655 20.192 43066 Z= 0.339 Chirality : 0.043 0.206 4774 Planarity : 0.004 0.081 5408 Dihedral : 6.243 84.346 4388 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 2.96 % Allowed : 21.41 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.33 (0.14), residues: 3910 helix: 0.94 (0.12), residues: 1906 sheet: -1.43 (0.24), residues: 417 loop : -1.26 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 675 TYR 0.035 0.002 TYR G1127 PHE 0.044 0.001 PHE G1141 TRP 0.041 0.002 TRP E1032 HIS 0.011 0.001 HIS H1059 Details of bonding type rmsd covalent geometry : bond 0.00979 (31840) covalent geometry : angle 0.65314 (43034) SS BOND : bond 0.00726 ( 16) SS BOND : angle 1.90748 ( 32) hydrogen bonds : bond 0.03774 ( 1574) hydrogen bonds : angle 4.76413 ( 4473) Misc. bond : bond 0.00400 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 434 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.7545 (mmm) cc_final: 0.7326 (mmm) REVERT: A 435 HIS cc_start: 0.6545 (t-90) cc_final: 0.5452 (m-70) REVERT: B 463 MET cc_start: 0.7139 (mmt) cc_final: 0.6499 (mmt) REVERT: B 527 MET cc_start: 0.8055 (tpp) cc_final: 0.7830 (tpt) REVERT: B 629 MET cc_start: 0.4537 (ppp) cc_final: 0.3791 (tpp) REVERT: B 721 MET cc_start: 0.7153 (ppp) cc_final: 0.5984 (ptp) REVERT: B 803 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7991 (mp) REVERT: C 97 ILE cc_start: 0.8280 (mp) cc_final: 0.7946 (mt) REVERT: C 178 ARG cc_start: 0.6384 (ttp80) cc_final: 0.6051 (ttp80) REVERT: C 199 ASP cc_start: 0.7424 (m-30) cc_final: 0.6824 (t0) REVERT: C 298 ASN cc_start: 0.7456 (t0) cc_final: 0.7039 (t0) REVERT: C 361 MET cc_start: 0.7660 (mmt) cc_final: 0.7182 (mmt) REVERT: C 414 MET cc_start: 0.6728 (ppp) cc_final: 0.6489 (pmm) REVERT: C 620 LEU cc_start: 0.8378 (tt) cc_final: 0.8152 (tt) REVERT: C 710 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: C 812 ILE cc_start: 0.7982 (pt) cc_final: 0.7764 (mt) REVERT: D 195 ASP cc_start: 0.8491 (t0) cc_final: 0.8105 (t0) REVERT: D 407 MET cc_start: 0.5767 (mmp) cc_final: 0.5542 (mmt) REVERT: D 463 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7363 (mmt) REVERT: D 721 MET cc_start: 0.6781 (ppp) cc_final: 0.6160 (ptp) REVERT: E 1021 SER cc_start: 0.8826 (m) cc_final: 0.8435 (p) REVERT: E 1041 THR cc_start: 0.5188 (OUTLIER) cc_final: 0.4908 (p) REVERT: E 1199 MET cc_start: 0.7914 (mtp) cc_final: 0.7701 (ttm) REVERT: G 1005 ARG cc_start: 0.7847 (mtp85) cc_final: 0.7546 (mtp180) REVERT: G 1033 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5197 (pp) REVERT: G 1082 PHE cc_start: 0.5013 (p90) cc_final: 0.4676 (p90) REVERT: G 1098 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.6751 (mtm110) REVERT: H 1022 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4803 (mm) REVERT: H 1064 ARG cc_start: 0.6070 (mpt180) cc_final: 0.5295 (mtm-85) REVERT: H 1139 ILE cc_start: 0.8095 (mm) cc_final: 0.7807 (mm) REVERT: H 1191 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7615 (ttm) outliers start: 99 outliers final: 78 residues processed: 510 average time/residue: 0.2185 time to fit residues: 180.0204 Evaluate side-chains 488 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 403 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 323 TRP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1009 MET Chi-restraints excluded: chain E residue 1039 CYS Chi-restraints excluded: chain E residue 1041 THR Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1115 PHE Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1033 LEU Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1105 ILE Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1194 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 269 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 286 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 159 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 381 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** E1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1008 GLN ** F1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1008 GLN ** H1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.196148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.164995 restraints weight = 53489.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165070 restraints weight = 80533.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.166478 restraints weight = 70480.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.167530 restraints weight = 45374.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.169482 restraints weight = 37721.057| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.230 31858 Z= 0.360 Angle : 0.679 20.168 43066 Z= 0.350 Chirality : 0.044 0.222 4774 Planarity : 0.004 0.093 5408 Dihedral : 6.187 83.140 4388 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 2.99 % Allowed : 21.68 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.33 (0.14), residues: 3910 helix: 0.96 (0.12), residues: 1905 sheet: -1.43 (0.24), residues: 413 loop : -1.29 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G1098 TYR 0.023 0.002 TYR G1088 PHE 0.046 0.002 PHE G1141 TRP 0.039 0.002 TRP B 130 HIS 0.009 0.001 HIS F1059 Details of bonding type rmsd covalent geometry : bond 0.00991 (31840) covalent geometry : angle 0.67688 (43034) SS BOND : bond 0.00656 ( 16) SS BOND : angle 2.02501 ( 32) hydrogen bonds : bond 0.03828 ( 1574) hydrogen bonds : angle 4.74508 ( 4473) Misc. bond : bond 0.00418 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 416 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.7556 (mmm) cc_final: 0.7337 (mmm) REVERT: A 435 HIS cc_start: 0.6584 (t-90) cc_final: 0.5408 (m-70) REVERT: B 463 MET cc_start: 0.7171 (mmt) cc_final: 0.6517 (mmt) REVERT: B 527 MET cc_start: 0.8001 (tpp) cc_final: 0.7784 (tpt) REVERT: B 629 MET cc_start: 0.4474 (ppp) cc_final: 0.3750 (tpp) REVERT: B 721 MET cc_start: 0.7241 (ppp) cc_final: 0.6101 (ptp) REVERT: B 803 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7968 (mp) REVERT: C 97 ILE cc_start: 0.8284 (mp) cc_final: 0.7941 (mt) REVERT: C 178 ARG cc_start: 0.6441 (ttp80) cc_final: 0.6088 (ttp80) REVERT: C 199 ASP cc_start: 0.7385 (m-30) cc_final: 0.6799 (t0) REVERT: C 298 ASN cc_start: 0.7487 (t0) cc_final: 0.7076 (t0) REVERT: C 361 MET cc_start: 0.7673 (mmt) cc_final: 0.7179 (mmt) REVERT: C 620 LEU cc_start: 0.8352 (tt) cc_final: 0.8146 (tt) REVERT: C 812 ILE cc_start: 0.7983 (pt) cc_final: 0.7770 (mt) REVERT: D 195 ASP cc_start: 0.8546 (t0) cc_final: 0.8158 (t0) REVERT: D 407 MET cc_start: 0.5734 (mmp) cc_final: 0.5533 (mmt) REVERT: D 463 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7235 (mmt) REVERT: D 721 MET cc_start: 0.6736 (ppp) cc_final: 0.6201 (ptp) REVERT: E 1021 SER cc_start: 0.8847 (m) cc_final: 0.8452 (p) REVERT: E 1041 THR cc_start: 0.5282 (OUTLIER) cc_final: 0.5003 (p) REVERT: E 1199 MET cc_start: 0.7978 (mtp) cc_final: 0.7777 (ttm) REVERT: F 1066 CYS cc_start: 0.2689 (t) cc_final: 0.2462 (t) REVERT: G 1005 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7502 (mtp180) REVERT: G 1033 LEU cc_start: 0.5515 (OUTLIER) cc_final: 0.5194 (pp) REVERT: G 1082 PHE cc_start: 0.5014 (p90) cc_final: 0.4692 (p90) REVERT: H 1022 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4936 (mm) REVERT: H 1064 ARG cc_start: 0.6090 (mpt180) cc_final: 0.5387 (mtm-85) REVERT: H 1139 ILE cc_start: 0.8110 (mm) cc_final: 0.7820 (mm) REVERT: H 1191 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7618 (ttm) outliers start: 100 outliers final: 86 residues processed: 490 average time/residue: 0.2061 time to fit residues: 164.8883 Evaluate side-chains 495 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 403 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 710 GLU Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 323 TRP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 549 TYR Chi-restraints excluded: chain D residue 790 SER Chi-restraints excluded: chain D residue 792 VAL Chi-restraints excluded: chain D residue 803 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain E residue 1009 MET Chi-restraints excluded: chain E residue 1039 CYS Chi-restraints excluded: chain E residue 1041 THR Chi-restraints excluded: chain E residue 1113 LEU Chi-restraints excluded: chain E residue 1134 ILE Chi-restraints excluded: chain E residue 1149 ILE Chi-restraints excluded: chain F residue 1033 LEU Chi-restraints excluded: chain F residue 1115 PHE Chi-restraints excluded: chain F residue 1120 CYS Chi-restraints excluded: chain F residue 1194 VAL Chi-restraints excluded: chain G residue 1033 LEU Chi-restraints excluded: chain G residue 1103 SER Chi-restraints excluded: chain G residue 1105 ILE Chi-restraints excluded: chain G residue 1129 THR Chi-restraints excluded: chain H residue 1011 LEU Chi-restraints excluded: chain H residue 1022 LEU Chi-restraints excluded: chain H residue 1033 LEU Chi-restraints excluded: chain H residue 1063 TRP Chi-restraints excluded: chain H residue 1066 CYS Chi-restraints excluded: chain H residue 1068 LEU Chi-restraints excluded: chain H residue 1115 PHE Chi-restraints excluded: chain H residue 1120 CYS Chi-restraints excluded: chain H residue 1131 HIS Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1194 VAL Chi-restraints excluded: chain H residue 1197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 268 optimal weight: 0.7980 chunk 318 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 384 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 358 optimal weight: 7.9990 chunk 295 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1148 ASN F1204 HIS G1008 GLN ** H1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.195455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164042 restraints weight = 53577.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164209 restraints weight = 82636.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.165540 restraints weight = 72322.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.166485 restraints weight = 46856.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.168441 restraints weight = 39224.837| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.230 31858 Z= 0.363 Angle : 0.692 20.212 43066 Z= 0.354 Chirality : 0.044 0.247 4774 Planarity : 0.004 0.057 5408 Dihedral : 6.110 82.420 4388 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 3.02 % Allowed : 21.74 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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 aren not related in a simple way. whole: -0.30 (0.14), residues: 3910 helix: 0.99 (0.12), residues: 1895 sheet: -1.45 (0.24), residues: 413 loop : -1.27 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G1098 TYR 0.039 0.002 TYR G1127 PHE 0.041 0.002 PHE G1141 TRP 0.041 0.002 TRP B 130 HIS 0.008 0.001 HIS E1131 Details of bonding type rmsd covalent geometry : bond 0.00997 (31840) covalent geometry : angle 0.69013 (43034) SS BOND : bond 0.00526 ( 16) SS BOND : angle 2.01638 ( 32) hydrogen bonds : bond 0.03876 ( 1574) hydrogen bonds : angle 4.75575 ( 4473) Misc. bond : bond 0.00439 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.05 seconds wall clock time: 96 minutes 57.95 seconds (5817.95 seconds total)